Compositions and methods for producing lipids and other biomaterials from grain ethanol stillage and stillage derivatives

ABSTRACT

Lipogenic yeasts bioengineered to overexpress genes for lipid production, and methods of use thereof. The yeasts are modified to express, constitutively express, or overexpress an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, an auxiliary activity family 9 enzyme, or combinations thereof. The yeasts in some cases are also modified to reduce or ablate activity of certain proteins. The methods include cultivating the yeast to convert low value soluble organic stillage byproducts into lipids suitable for biodiesel production and other higher value uses.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with Government support under IIP 1520485 and IIP 1632255 awarded by the National Science Foundation. The Government has certain rights in this invention.

FIELD OF THE INVENTION

The invention is directed to engineered yeasts and methods for converting stillage organics into lipids and other biomaterials.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. The ASCII copy, created on Aug. 11, 2017, is named USPTO—200421—SEQUENCE_LISTING_ST25.txt and is 401,461 bytes in size.

BACKGROUND

Renewable fuels are environmentally desirable, especially fuels with higher energy density such as biodiesel. U.S. biodiesel production capacity however, is underused. From January of 2014 to July 2016, annual production of biodiesel did not exceeded 60% of plant capacity. This was due in part to a lack of inexpensive feedstock supply, which the industry greatly needs as an alternative source of seed oils (Anon 2016).

Plant triglycerides from soybeans, canola, rapeseed and palm oil can be converted into methyl or ethyl esters for use as biodiesel. Biodiesel produced in the U.S. is mainly derived from waste cooking oils, the edible oils of soybean and rapeseed (canola) (Hammond et al. 2005), from the inedible corn oil recovered following fermentation and distillation of grain to ethanol, and with lesser amounts generated from animal fats.

If the U.S. were to use all of its domestic soybeans to make biodiesel, it would result in about 5.1 billion gallons of biofuel. This approach, however, is not realistic because these oilseeds are also key components of the food chain and are used for the production of many household and industrial products. Thus, increasing the production of biodiesel from foodstuffs would lead to higher prices of commodities derived from them, and economic hardship for the consumer.

Biodiesel can be made from the triglycerides generated by oleaginous (lipogenic) yeast or algae. In fact, 2 to 3 times more lipid/g dry weight is generated by these microbial sources than from seed oils. Certain algae can accumulate lipids when cultivated on sunlight and CO₂, but fixation of CO₂ by photosynthesis requires a great deal of metabolic energy, so cell growth and lipid accumulation is relatively slow. Some algae can grow heterotrophically on simple organic compounds dissolved in water, which greatly increases their rates of lipid accumulation. Algae, however, do not generally assimilate more complex organic materials such as starch, cellulosic or hemicellulosic oligomers. Ascomyceteous and basidiomyceteous lipogenic yeasts and filamentous fungi will, however, readily assimilate these compounds. Moreover, because these yeasts and fungi are heterotrophic, their growth rates on simple or complex dissolved organic materials are much faster than algae cultivated under heterotrophic conditions.

If it were possible to produce biodiesel from cellulosic residues or other waste organic materials in yields similar to what could be achieved with ethanol production, domestic biodiesel production could satisfy a significant fraction of the national transport energy demand without affecting the food supply. Furthermore, this increased domestic production would also decrease dependency on foreign oil.

Agricultural residue (e.g. corn stover) is a potential source of renewable biomass that could be converted into liquid transportation fuels such as biodiesel if recalcitrance of the biomass to hydrolysis, the presence of inhibitors mixed with the hydrolyzed sugars, and the difficulty in obtaining microbial catalysts that will convert the sugars to lipids in high yield can be overcome. The potential for biodiesel production from agricultural residues is significant. If the residues from U.S. soybean production alone were collected and converted by a microbial process with a mass yield of 35% based on the starting sugar, it would be possible to produce about 10 million metric tons of lipid annually or about 15% more oil than the total of what is presently recovered from the processing of soybeans itself.

Cellulosic biodiesel produced by a lipogenic yeast cultivated on agricultural hydrolysate would generate an animal feed byproduct similar to that obtained from processing oil from soybeans or palm oil. Based on comparisons with existing prices for wholesale yeast protein from brewing, biodiesel production by lipogenic yeast would yield residual yeast protein with the same or slightly higher market value as soy protein.

While several technologies exist to pretreat and enzymatically saccharify agricultural residues for hydrolysis to create fermentable sugars, new microbial biocatalysts are needed to convert the resulting mixed sugars into lipids and other higher value materials.

Grain ethanol plants are a potential source of unused, soluble and insoluble organic materials suitable for biodiesel production. In wet and dry-mill ethanol operations, cornstarch is enzymatically converted into sugar then fermented to ethanol. The process leaves behind significant amounts of corn fiber and generates soluble organics as byproducts of ethanol production.

Grain ethanol plants are becoming less economical to operate due to lack of demand for ethanol and to low profit margins when grain prices are high and petroleum prices are low. Ethanol derived from grain is also criticized for having poor compatibility with fuel distribution systems, reducing the food supply, contributing to soil erosion, and releasing net CO₂ emissions that are only marginally better than gasoline. Reduced operating costs, increased process efficiency, better fuel compatibility, and higher product value and diversity could significantly improve the economics and environmental acceptability of this process.

In a conventional dry mill process, whole grain is hammer milled, then steam treated in a jet cooker as it is sent to the fermentation tank for liquefaction with a thermostable alpha-amylase. Following cooling and saccharification, the mash is inoculated for fermentation. Variations on this basic process can involve separation of corn hulls (fiber), starch and germ gluten (protein) prior to saccharification, use of less steam for cooking, use of raw starch, recovery of edible corn oil from the germ and other changes. Following fermentation, ethanol is recovered by distillation, and the bulk of the fiber and protein, along with yeast cells and corn oil, are separated from the dissolved organics by centrifugation. This yields wet cake or distiller's wet grain (DWG) solids and thin stillage (TS) solubles. In a conventional process, the distiller's wet grain is dried to make distiller's dried grain (DDG) and the thin stillage containing the solubles (S) is evaporated to make a syrup, which is sprayed back onto the distiller's dried grain to make DDGS. Evaporation of the thin stillage separates a fraction of the inedible corn oil, which can be recovered for biodiesel production (FIG. 1).

Stillages (vinasse) following distillation of ethanol from industrial ethanol fermentations of grain include corn gluten and yeast protein, residual corn fiber, yeast cells, corn oil, and dissolved organics. Thin stillage contains significant quantities of glycerol (14 to 20 g/l), glucose disaccharides (e.g., cellobiose, trehalose, etc.) (6 to 10 g/l), xylose, lactic acid, corn oil and various oligosaccharides derived from residual undigested starch, dextrins, cellulose and hemicellulose. The total dissolved and suspended organic content of thin stillage is about 10% w/v. Table 1 presents a published summary of stillage components (Kim et al. 2008).

TABLE 1 Exemplary Stillage Composition Stillage Component g/l Glucose 0.9 Glucan (oligosaccharide) 12.4 Xylose 0.7 Xylan (oligosaccharide) 3.7 Arabinose 0.4 Arabinan (oligosaccharide) 0.5 Lactic acid 16.8 Glycerol 14.4 Acetic acid 0.3 Butanediol 1.9 Ethanol 0.6

The glycerol and oligosaccharide contents of thin stillage retain water during evaporation and prevent drying. This makes thin stillage evaporation energy-inefficient.

Removing glycerol and oligosaccharides prior to evaporation is therefore desirable. Stillages from other ethanol distillation processes also present disposal problems. Stillage is difficult and non-economical to treat in a waste water system because of its high biological oxygen demand (BOD), its high organic content and low pH. Stillage can also have relatively high nitrogen and phosphorous contents, about 2 g/l and 130 mg/l respectively (Yen et al. 2012). The massive volumes of thin stillage resulting from fuel ethanol production are particularly difficult to handle. A significant fraction of the thin stillage is therefore recycled or “backset” into the liquefaction stage, which increases the level of dissolved organics in the fermentation and whole stillage.

Methods and tools for converting on-site low value soluble organic stillage byproducts from ethanol production into biodiesel are needed to increase fuel production without harvesting more grain. Such methods and tools would reduce the organic load in the backset while creating higher value products such as yeast oil, enzymes, and animal feed from underutilized organic byproducts.

SUMMARY OF THE INVENTION

The invention addresses the aforementioned needs by providing engineered yeasts and methods for converting stillage organics into lipids and other biomaterials.

An exemplary method of the invention for converting stillage organics into yeast oil, cell protein, and enzymes is shown in FIG. 2. This method is similar to standard dry mill operations up through the centrifugation of whole stillage to separate thin stillage (TS) and distiller's wet grain (DWG). Instead of sending thin stillage directly to evaporation, however, oil (e.g., corn oil) is first removed. Second stage thin film evaporators then remove 50 to 80% of the water, and residual protein is separated. The clarified, concentrated thin stillage (CTS) is used as a medium to cultivate native or bioengineered lipogenic yeasts that produce enzymes that will accelerate liquefaction of starch, rapidly consume glycerol, cellobiose, trehalose xylose, lactic acid and residual oligosaccharides while accumulating yeast lipids and biomass. An advantage of microbial bioconversion is that a glycerol byproduct generated during conversion of triglycerides to biodiesel can be fed back into the bioreactor to increase both the rate and yield of lipid production.

An amylolytic, lipogenic yeast specifically bioengineered for rapid lipid and enzyme production from dissolved organics in the clarified thin stillage and other stillage forms is preferred for use in this process. The yeasts are modified to express, constitutively express, or overexpress an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme, or any combination thereof. The yeasts are in some cases also modified to reduce or ablate activity of other enzymes. The bioengineered yeasts of the invention produce enzymes that accelerate liquefaction of starch, rapidly consume glycerol, cellobiose, trehalose, xylose, lactic acid and residual oligosaccharides while accumulating yeast lipids.

The technology described herein can increase profit margins for grain ethanol producers by making higher value and more diverse byproducts. The technology also has the added benefits of decreasing thin stillage viscosity, increasing protein production, reducing organic load from wastewaters, reducing natural gas-based processing expenses, and, in some cases, releasing a larger fraction of corn oil from the dried grain solids. Hence, the technologies would be of interest to several industries by providing a means to diversify products and increase the supply of high energy density renewable fuels while at the same time reducing environmental pressures.

The objects and advantages of the invention will appear more fully from the following detailed description of the preferred embodiment of the invention made in conjunction with the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schema of a conventional dry mill ethanol process.

FIG. 2 shows a schema of a process of the present invention for converting stillage organics into yeast oil, protein, and enzymes.

FIG. 3 shows a schema of intermediary metabolism linked to fatty acid biosynthesis in yeast. PDH, pyruvate dehydrogenase; PYC Pyruvate carboxylase; Ac, aconitase; ME malic enzyme; MDc malate decarboxylase, cytosolic; MDm malate dehydrogenase, mitochondrial; ACL ATP:citrate lyase; ACC, acetyl-CoA carboxylase; ICDH, isocitrate dehydrogenase; FAS, fatty acid synthase; DGA, diacylglycerol acyltransferase. a, b, c and d are transporters.

FIG. 4 shows a graph of the effects of different culture media on basal lipid content of Lipomyces starkeyi type strain NRRL Y-11557. The effects of six types of culture media on L. starkeyi basal lipid production were evaluated. YPD is yeast peptone dextrose media. M1 (LN) is a minimally defined, low nitrogen media containing yeast nitrogen base and supplemented with urea, M2 (LN) is a low nitrogen media having the same components as YPD but containing only 3.64% and 1.82% of the yeast extract and peptone contained in YPD. M3 (HN) and M4 (HN) are the high nitrogen containing versions of M1, with M4 HN containing peptone. mTS is modified thin stillage, prepared by clarifying and concentrating ethanol thin stillage. Results are shown as normalized fluorescence to OD630.

FIG. 5 is a diagram of a base vector used for creating genomic integrating cassettes. The origin of replication (Ori) and kanamycin resistance gene (Kan R) permit propagation and maintenance in E. coli. Two multiple cloning sites (MCSs) enable insertion of gene target cassettes adjacent to loxP sites (Xs), which flank an expression cassette for nourseothricin resistance (NAT R) driven by the constitutive TDH3 promoter (TDH3p) and terminator (TDH3t). Digestion of the vector with AsiS1 enables linearization and integration into the yeast genome. The sequence of the base vector is represented by SEQ ID NO:91.

FIG. 6 shows a schema of a screening pipeline used for generating metabolically engineered yeast.

FIG. 7 shows growth of various strains of L. starkeyi on glucose as the sole carbon source (left panel) or glycerol as the sole carbon source (right panel).

FIGS. 8A and B show Nile Red screening of yeast transformants in YPD or mTS. Results are shown normalized to the wild-type and OD600 after two (YPD) or three (mTS) days of growth. FIG. 8A shows averages of the top 50% of transformants with each gene in preliminary screening. Of 234 transformants cultivated, preliminary screening revealed three strains transformed with three genes (cDGA1-1233, cDGA1-1389, and cACC1) that showed large standard deviations or higher means than the base vector transformed strains. Data is shown for the end of the growth phase in each media (YPD=2 days, mTS=3 days). FIG. 8B shows results of a validation screen of the prime performers of each gene in mTS evaluated in triplicate, revealing that the transformants DGA1-1233 6L, GUT1-1602 6L, and GUT1-1617 2L show superior lipid accumulation over the WT as deemed by Nile Red fluorescence.

FIG. 9 shows consumption of organics and cell density of wild-type L. starkeyi (Ls-1) and a GUT1 engineered strain (Ls-11). The presence of glycerol, xylitol, cellobiose, lactic acid, and arabinose in 200 mL of mTS solution in shake flasks were monitored by HPLC analysis during cultivation of wild-type L. starkeyi (Ls-1) and a strain with an engineered version of the glycerol kinase gene (GUT1 Ls-11). Cell density (OD600) and direct cell counts were also determined. In this experiment, the Ls-11 engineered strain achieved higher cell density and consumed more glycerol than the wild-type strain.

FIGS. 10A and 10B show a difference in the cellular morphologies of wild-type L. starkeyi (FIG. 10A) and a strain overexpressing GUT1 (FIG. 10B) when cultured on mTS. Besides generating larger liposomes in some cells, the strain overexpressing GUT1 also formed cellular assemblies similar to pseudomycelium. Photos were taken after two days of growth in mTS.

FIGS. 11A-11C show a comparison of wild-type L. starkeyi with engineered strain DGA1-1233 6L comprising the DGA1-1233 gene. FIG. 11A shows growth rates and carbon utilization of wild-type (solid shapes) and DGA1-1233 6L (open shapes) of glycerol and cellobiose. Cultures were grown in triplicate on mTS media, error bars denote the standard deviation. FIGS. 11B and 11C show cellular morphologies for wild-type (FIG. 11B) and DGA1-1233 6L (FIG. 11C), showing significantly more liposomes in DGA1-1233 6L.

FIGS. 12A and 12B show Nile Red fluorescence and percent lipid analysis of wild-type L. starkeyi and the engineered strain designated DGA1-1233 6L cultured in mTS using bioreactors. FIG. 12A shows relative Nile Red fluorescence of the wild-type strain and the DGA1-1233 transformant measured at different time points. Spent media was drawn off and the bioreactors refilled with thin stillage after 48 hours of growth. FIG. 12B shows percent lipid content of cell dry weight of wild-type L. starkeyi and the DGA1-1233 transformant. The engineered DGA1-1233 6L strain had more than double the Nile Red fluorescence and percent lipid content.

FIG. 13 shows a comparison of strains overexpressing DGA1 variants in synthetic thin stillage medium (sTS) by Bodipy fluorescence. A) Bodipy fluorescence of the wild-type Ls-1 (black), gDGA1 163M (dark gray), cDGA-1233 6L (light gray), and cDGA 154L (white) L. starkeyi transformants as monitored over the course of 4 days (denoted as D1, D2, D3, and D4). The cDGA 154L strain was chosen as the platform strain for further improvement due to its similar performance to cDGA 6L and Hygromycin B resistance marker.

FIG. 14 shows dilution-corrected Bodipy fluorescence in mutant and wild-type Acc1-transformed L. starkeyi. The S1146 point mutation increases fluorescence values relative to the wild-type strain, whereas S639A and the double mutation leads to slightly inferior performance. Data is plotted as the average difference in fluorescence from the untransformed wild-type strain over the course of four days from 63-188 transformants in each pool.

FIG. 15 shows dilution-corrected Bodipy fluorescence in wild-type and SCT1-transformed L. starkeyi. Average wild-type fluorescence, average transformant fluorescence, SCT1 110L transformant fluorescence, and transformant SCT1 131L fluorescence are shown. In FIG. 15, as well as in FIGS. 16, 24, 25, and 27, there are no error bars included with the data for the single transformants because each data point represents fluorescence from one culture of each transformant.

FIG. 16 shows dilution-corrected Bodipy fluorescence in wild-type and SLC1-transformed L. starkeyi. Average wild-type fluorescence, average transformant fluorescence, and SCT1 30L transformant fluorescence are shown.

FIG. 17 shows dilution-corrected Bodipy fluorescence with dual overexpression of DGA1 and the gene for the deregulated protein Acc1(S1146A) in L. starkeyi. Dilution corrected Bodipy fluorescence of wild-type strain (black), the strain overexpressing cDGA1 (dark gray), and the strain in which overexpressed cDGA1 was crossed with Acc1(S1146A) overexpressing strains was monitored over the course of 4 days (D1, D2, D3, and D4). The mated strain was obtained by crossing the top performers from each cDGA1 and Acc1(S1146A) transformant pool. Overexpression of both the DGA1 gene and the gene for the mutated protein Acc1(S1146A) synergistically enhanced lipid accumulation compared to overexpression of each gene alone.

FIG. 18 shows dilution-corrected Bodipy fluorescence of L. starkeyi strains with combinatorial expression of lipogenic cassettes. The strains are shown in the following order (from left (black) to right (white): wild-type, cDGA-NAT (the top cDGA1-1233 strain), cDGA-HPH (a new platform strain), and cDGA-HPH crossed with either cDGA-NAT or a strain transformed with engineered SCT1. Fluorescence was monitored over the course of 4 days (D1, D2, D3, and D4). The top strains (lightest gray and white) exhibited improvement in lipid production through dual overexpression of lipogenic cassettes.

FIG. 19 shows dilution-corrected Bodipy fluorescence of L. starkeyi strains with combinatorial expression of lipogenic and auxiliary cassettes. The strains are shown in the following order (from left (black) to right (white): wild-type, ATP citrate lyase α and β subunit overexpressing strain (designated as cAcl1/2), malic enzyme cloned from gDNA overexpressing strain (designated as gMalic Enzyme), diacylglycerol transferase (designated as cDGA1-1233) cloned from cDNA overexpressing strain (cDGA1), combinatorial cDGA1-1233 and Acl1/2 overexpressing strain (cDGA1×cAcl1/2), and combinatorial cDGA1-1233 and genomic malic enzyme overexpressing strain (cDGA1×gMalic Enzyme). Combinatorial expression of lipogenic and auxiliary cassettes improved lipid production.

FIG. 20 shows Bodipy analysis in sTS of a lipogenic diacylglycerol transferase overexpressing strain (cDGA) and the same strain transformed with a second base vector. The introduction of expressing a second resistance marker does not increase lipid accumulation on its own, and may even decrease lipid levels.

FIG. 21 shows wild-type L. starkeyi (first column), or transformed cells overexpressing the gene for glycerol kinase (GUT1, second column) or GUT1 and an FAD-dependent glycerol-3-phosphate dehydrogenase (GUT1/GUT2, third column) plated onto YP solid media containing 2% glycerol and incubated for 4-5 days at 30° C. The growth defect of the GUT1 single transformant was rescued by overexpression of GUT2.

FIG. 22 shows average dilution-corrected Bodipy fluorescence in a parental wild-type L. starkeyi strain (black), a strain overexpressing GUT2 (dark gray), a strain overexpressing GUT1 (light gray), and a GUT1/GUT2 double transformant (white). The GUT1/GUT2 double transformant accumulates more lipid than parental wild-type or GUT1 overexpressing strains. Overexpression of GUT2 alone has little effect on lipid accumulation.

FIGS. 23A-23C show cell density (OD), glucose consumption, and glycerol consumption in a parental wild-type L. starkeyi strain (FIG. 23A), a GUT1 single transformant (FIG. 23B), and a GUT1/GUT2 double transformant (FIG. 23C). FIG. 23D shows superimposed curves of glycerol utilization in the wile-type strain and the GUT1/GUT2 double transformant. Glycerol was depleted in just 67 hours in the GUT1/GUT2 double transformant versus 84 hours in the wild-type strain.

FIG. 24 shows dilution-corrected Bodipy fluorescence of wild-type L. starkeyi (black) and a pool of GPD1 transformants (gray). Bodipy fluorescence was monitored in synthetic thin stillage over the course of 4 days. Overall, the transformants exhibited moderately higher fluorescence over the wild-type, with almost 13% improvement on the fourth day. The top transformant GPD1 67M (white) is also shown. The data indicate that overexpression of glycerol-3-phosphate in L. starkeyi increases lipid production.

FIG. 25 shows dilution-corrected Bodipy fluorescence in wild-type L. starkeyi and GND1/ZWF1 transformants. Average wild-type fluorescence, average transformant fluorescence, transformant GND1+ZWF1 37L fluorescence, and transformant GND1+ZWF1 26L fluorescence are shown.

FIG. 26 shows dilution-corrected Bodipy fluorescence in wild-type L. starkeyi and FOX1 and PDX1 knockouts.

FIG. 27 shows dilution-corrected Bodipy fluorescence in wild-type L. starkeyi and DGA2 transformants. Average wild-type fluorescence, average transformant fluorescence, transformant DGA2 20L fluorescence, and transformant DGA2 70L fluorescence are shown.

FIG. 28 shows an engineered yeast constitutively secreting a glucoamylase that retains activity following incubation for 1 hour at 70° C. A) Supernatant of a wild-type L. starkeyi culture conditioned to secrete enzyme incubated on 1% corn starch plates prior to (top) or after (bottom) boiling. The presence of a clearing zone indicates starch hydrolytic activity, which is lost after boiling. B) Supernatant of wild-type cells display glucoamylase activity when cultured in starch containing media, but not YPD (left two boxes). In this case, starch hydrolysis is indicated by a zone impervious to iodine staining on a 2% starch plate. The supernatant of the engineered strain exhibits activity when cultured on both YPD and starch containing media, and is retained following incubation for one hour at 70° C. (right two boxes).

DETAILED DESCRIPTION OF THE INVENTION

The elements and method steps described herein can be used in any combination whether explicitly described or not.

All combinations of method steps as used herein can be performed in any order, unless otherwise specified or clearly implied to the contrary by the context in which the referenced combination is made.

As used herein, the singular forms “a,” “an,” and “the” include plural referents unless the content clearly dictates otherwise.

Numerical ranges as used herein are intended to include every number and subset of numbers contained within that range, whether specifically disclosed or not. Further, these numerical ranges should be construed as providing support for a claim directed to any number or subset of numbers in that range. For example, a disclosure of from 1 to 10 should be construed as supporting a range of from 2 to 8, from 3 to 7, from 5 to 6, from 1 to 9, from 3.6 to 4.6, from 3.5 to 9.9, and so forth.

All patents, patent publications, and peer-reviewed publications (i.e., “references”) cited herein are expressly incorporated by reference to the same extent as if each individual reference were specifically and individually indicated as being incorporated by reference. In case of conflict between the present disclosure and the incorporated references, the present disclosure controls.

All protein identification (PID) numbers provided herein refer to proteins in the database of the Joint Genome Institute (JGI) of the United States Department of Energy. See, e.g., Jeffries 2013.

It is understood that the invention is not confined to the particular construction and arrangement of parts herein illustrated and described, but embraces such modified forms thereof as come within the scope of the claims.

Lipogenic (Oleaginous) Yeasts

An aspect of the invention encompasses bioengineered yeasts. The bioengineered yeasts are preferably derived from lipogenic yeasts. The methods of the invention are preferably performed with either native, non-bioengineered lipogenic yeasts or bioengineered lipogenic yeasts.

Lipogenic yeasts (also known as oleaginous yeasts) have been recognized for more than 50 years. They are defined as those that accumulate lipids in intracellular oil bodies to greater than 20% of their dry mass. In some yeasts, lipids have been reported to account for up to 71% of the cell's total biomass (Holdsworth et al. 1988). Out of the 1200 to 1500 known yeast species, only a fraction qualifies as lipogenic. Lipomyces starkeyi was among the earliest lipogenic yeasts studied (Lodder et al. 1952). Other known lipogenic yeasts include Yarrowia lipolytica (Papanikolaou et al. 2001), and species in the genera of Rhodotorula, Cryptococcus (Ratledge 2002), Candida, Trichosporon (Holdsworth et al. 1988), Rhodosporidium, Sporidiobolus, Sporodobolomyces, and various other ascomyceteous and basidiomycete genera amounting for a total of about 100 species (Garay et al. 2016).

Lipogenic yeasts belong to the larger taxonomic groups of filamentous ascomyceteous and basidiomycetous fungi. Exemplary lipogenic yeasts include yeasts from the genus Lipomyces, such as L. starkeyi, L. anomalus, L. arxii, L. chichibuensis, L. doorenjongii, L. japonicus, L. kockii, L. kononenkoae, L. lipofer, L. mesembrius, L. oligophaga, L. orientalis, L. smithiae, L. spencermartinsiae, L. suomiensis, L. tetrasporus, L. yamadae, L. yarrowii, and L. Sp.; yeasts from the genus Yarrowia, such as Y. lipolytica, L. bubula, Y. deformans, Y. divulgata, Y. keelungensis, Y. porcina, Y. yakushimensis, and Y. Sp.; yeasts from the genus Candida, such as C. Sp.; yeasts from the genus Hansenula, such as H. polymorpha; yeasts from the genus Cunninghamella, such as S. bigelovii sp nov CGMCC 8094, S. echinulate, S. blakesleeana JSK2, and S. Sp. Salicorn 5; yeasts from the genus Mortierella, such as M. alpina, M. isabellina, and M. Sp.; yeasts from the genus Rhodosporidium, such as R. toruloides, R. babjevae, R. diobovatum, R. fluviale, R. kratochvilovae, R. paludigenum, R. sphaerocarpum, R. araucariae, R. colostri, R. dairenensis, R. graminis, R. lusitaniae, and R. mucilaginosa; yeasts from the genus Sporidiobolus, such as S. johnsonii, S. pararoseus, S. ruineniae, S. ruineniae, and S. salmonicolor; yeasts from the genus Sporobolomyces, such as S. bannaensis, S. beijingensis, S. carnicolor, S. metaroseus, S. odoratus, S. poonsookiae, S. singularis, and S. inositophilus; yeasts from the genus Occultifur, such as O. externus; yeasts from the genus Rhodotorula, such as R. bogoriensis, R. hylophila, R. glutinis, and R. rhodochrous; yeasts from the genus Trichosporon, such as T. fermentans, T. oleaginosus ATCC 20509, and T. cutaneum; and yeasts from the genus Cryptococcus, such as C. curvatus and C. Sp.

Certain filamentous fungi and unicellular algae can also be lipogenic. These include filamentous fungi from the genus Aspergillus, such as A. nidulans, and from the genus Mucor, such as M. circinelloides and M. rouxii. Lipogenic algae include species from the genus Scenedesmus, such as S. quadricauda.

Nontraditional lipogenic yeasts have an innate ability to convert poorly metabolized wastes from ethanol fermentation into lipids, protein, and enzymes. Some lipogenic yeasts naturally make large amounts of lipids from a wide variety of carbon sources, and this prodigious capacity renders them amenable to many bioprocessing applications.

Lipomyces starkeyi is a particularly preferred lipogenic yeast in this regard. L. starkeyi can utilize many different substrates, including the oligosaccharides and sugars found in both agricultural waste products and the hydrolysates of lignocellulosic material (Calvey et al. 2014, Gong et al. 2012, Zhao et al. 2008).

L. starkeyi genes of notable importance include 24 glycoside hydrolases, three alpha-amylases, a highly versatile dextranase to metabolize the lateral starch side chains, and 15 copies of maltase that convert oligosaccharides into glucose (Riley et al. 2016, Kang et al. 2005). Overproduction and secretion of the thermostable alpha-amylase and dextranase found in L. starkeyi are particularly useful for starch saccharification in the integrated process described here (FIG. 2).

The L. starkeyi genome also encodes at least two secreted β-1,4-glucosidases and four non-secreted β-1,4-glucosidases, all of which have cellulosic carbohydrate binding domains, and at least two endo-1,4-β-D-glucanases (cellulases) (Chen et al. 2008). These enzymatic activities are useful for hydrolyzing corn fiber or other agricultural residues for additional ethanol or biodiesel production.

An ensemble of lipogenic genes are found in the genome of L. starkeyi, along with the metabolic machinery to supply the acetyl-CoA and NADPH needed to support high levels of lipid biosynthesis. For example, L. starkeyi has two complete genes for pyruvate carboxylase (LsPYC1, LsPYC2). This enzyme combines CO₂ with pyruvate to make oxaloacetate, which in turn citrate synthase (LsCIT1, LsCIT2, LsCIT3) combines with acetyl-CoA to make citrate. Genes coding for the alpha and beta subunits of ATP:citrate lyase (LsACL1, LsACL2) are found in a tandem bidirectional operon. Likewise, the genome of L. starkeyi codes for two complete fatty acid synthase complexes (LsFAS1.1, LsFAS1.2; LsFAS2.1, LsFAS2.2) with each organized into tandem bidirectional operons. Most yeasts and fungi have only a single FAS complex with the alpha and beta-subunits occurring in different parts of the genome. Mitochondrial NAD-dependent malate dehydrogenase (MDm, LsMDH2; PID_5229), and cytosolic NAD-dependent malate dehydrogenase (MDc, LSMDH1; PID_3988) exist as single copies in wild type L. starkeyi. Tandem bidirectional operons or clusters of metabolically associated genes indicate close interdependence and coordinated regulation of genes comprising a metabolic trait (Jeffries 2013).

L. starkeyi yeast maintains a basal lipid content that increases throughout fermentation, which already meets or exceeds that of any other native lipogenic yeast or alga. The lipid profile produced by L. starkeyi is remarkably similar to that of palm oil, one of the most common biodiesel feedstocks, which indicates that a biodiesel produced from this species naturally has desirable fuel properties (Calvey et al. 2016).

L. starkeyi is generally regarded as safe (GRAS) and is easily propagated, rendering residual cells and cell proteins useful for fortifying livestock or other animal feeds (Collett et al. 2014). Lastly, its genome has been sequenced, which enables the use of rational metabolic engineering methodologies to target specific genes for overexpression or deletion. By simply altering the expression or regulation of genes already present in the genome it is possible to improve lipid production and accumulation on poorly utilized substrates or under conditions when lipogenesis would not normally occur.

Lipomyces starkeyi is among the yeasts that can metabolize glucose, xylose and cellobiose, which are the main sugars released from the hydrolysis of lignocellulosic materials (Pan et al. 2009). With L. starkeyi, optimal lipid production is attained when growing on a 2:1 mixture of glucose and xylose, the same ratio found in enzymatic hydrolysates. Some strains of L. starkeyi also produce lipid from glycerol.

The lipid profile of Lipomyces is similar to that of palm oil (Calvey et al. 2016), which is important for both food and fuel production. By developing technology that uses Lipomyces to produce biofuels from the hydrolysates of agricultural cellulosic residues as an alternative to seed-based oils, the present invention provides for generating fuel from a renewable, environmentally benign resource that does not compete with food production. Furthermore, biodiesel derived from non-food sources such as lignocellulosic hydrolysate is advantageous because it meets the criteria delineated under Renewable Fuel Standard 2 (RFS2), which mandates the increased use of advanced cellulosic biofuels.

In addition to yeasts, a large number of eukaryotic algae also accumulate lipids, particularly when cultivated under heterotrophic conditions (U.S. Pat. No. 8,110,670). These eukaryotic algae can also be used in the methods of the present invention. One advantage to using lipogenic yeasts over algae, however, is that they can be grown readily in bioreactors and, unlike heterotrophically cultivated lipogenic algae, lipogenic yeasts can be cultivated on a wide range of organic substrates.

Lipid accumulation typically occurs when a readily assimilated carbon source is present in excess and nitrogen is limiting (Wei et al. 2009, Zhu et al. 2012). For example, when L. starkeyi transitions into a nitrogen-limited environment the biosynthetic pathways dependent on abundant nitrogen shut down and lipogenesis becomes the dominant metabolic feature of the cell. The cells continue to assimilate carbon, and in the absence of new cell growth, they store it as triacylglycerols. The most readily assimilated lipogenic carbon source is typically glucose (Ratledge 2002), and xylose has been reported to increase lipid accumulation even more (Gong et al. 2012, Zhao et al. 2008). Other substrates include cellobiose, glycerol, oligosaccharides, various industrial organic byproducts and hydrolysate from non-edible cellulosic feedstocks (Vicente et al. 2010). The yeasts engineered herein are capable of producing lipid when glucose is limited and carbon organics and nitrogen are in abundance.

Any or all of the genes described above can be driven by promoters that may be regulated or constitutive, strong, moderately strong or weak in L. starkeyi to modulate their activity therein. Alternately these genes may be deleted or inactivated. Likewise genes for metabolic pathways competing with the desired product of the genes described above may be modulated, deleted, or inactivated in order to improve the desired product or its formation rate.

Any or all of the genes described above in L. starkeyi can be incorporated in any other lipogenic yeast to confer similar benefits therein.

Biochemistry of Lipid Synthesis by Yeasts

The biochemistry of lipid synthesis by yeasts is outlined in FIG. 3. Pyruvate is transported from the cytosol into the mitochondrion where pyruvate carboxylase (PYC) combines CO₂ with pyruvate to make oxaloacetate, and pyruvate dehydrogenase (PDH) oxidizes pyruvate to acetyl-CoA and NADH. Citrate synthase (CIT) combines with acetyl-CoA to make citrate while mitochondrial malate dehydrogenase (MDm) reduces oxaloacetate to malate.

The first step in response to nitrogen limitation is the activation of AMP deaminase, which cleaves adenosine monophosphate (AMP) into inosine monophosphate (IMP) and ammonia (NH₄). This activation lowers the intracellular concentrations of AMP, which inhibits the TCA cycle at the level of isocitrate dehydrogenase (ICDH), whose function is uniquely dependent on AMP in lipogenic yeasts (Ratledge 2004).

Significant evidence exists to support this mechanism. Intracellular AMP concentrations fall 11-fold within 24 hours after a transition to nitrogen limitation (Boulton et al. 1983). Also, assays of the Lipomyces ICDH1/2 enzyme show that its activity decreases about 5-fold when cells are transferred to a nitrogen-limiting medium (Tang et al. 2009). Activation of AMP deaminase and decreases in ICDH activity result in the accumulation of isocitrate and citrate (Boulton et al. 1983, Tang et al. 2009). Furthermore, lipid-accumulating Lipomyces cells display higher ACL enzymatic activity than proliferating cells (Naganuma et al. 1987).

When ICDH is no longer active, but the flux of glycolysis to pyruvate continues, isocitrate accumulates in the mitochondria and then equilibrates with citrate via isomerization. Citrate is exported into the cytosol via the citrate efflux system, which transports citrate out of the mitochondria in exchange for malate. The reduction in NADH formation by ICDH also results in less need for oxygen uptake and a lower rate of ATP synthesis.

Next, ATP:citrate lyase (ACL) catalyzes the cleavage of citrate into oxaloacetate and acetyl-CoA. This reaction is thought to be the primary source of the acetyl-CoA used for lipid synthesis and has been recognized as a key to efficient lipid production in lipogenic yeasts. ACL occurs in all lipogenic yeasts, but not in non-oleaginous species, which suggests a central role in lipid accumulation (Ratledge 2002, Evans et al. 1985). In the presence of CoA and ATP this enzyme cleaves citrate to acetyl-CoA and oxaloacetate, and supplies acetyl-CoA for lipid synthesis (Ratledge 1987). ACL is a dimeric protein with alpha and beta-subunits coded for by ACL1 and ACL2, which occur in a tandem bidirectional operon in the Lipomyces starkeyi genome (Jeffries 2013). The holoenzyme has a high affinity for citrate and ATP and is inhibited by ADP, glucose 6-phosphate, palmitoyl-CoA, and oleoyl-CoA. These allosteric inhibitors indicate that low ATP levels, high glycolytic flux, and the accumulation of fatty acid end products limit activity. The oxaloacetate formed by ACL can be converted to malate by a cytosolic malate dehydrogenase (MDc) and thus facilitate the export of more citrate from the mitochondrion.

Malate can also undergo conversion by malic enzyme (ME) into pyruvate and CO₂, while regenerating NADPH in the cytosol. The NADPH produced by the action of malic enzyme is thought to be the primary provider of reducing power for both fatty acid biosynthesis and desaturation reactions (Wynn et al. 1999). Lipid production may, however, draw on sources of NADPH in the cell such as the oxidative pentose phosphate pathway (Ratledge 2014). Specifically, two molecules of NADPH are required for each acetyl-CoA added to the growing fatty acyl chain during the standard fatty acid elongation cycle on the fatty acid synthase (FAS) complex (Ratledge 2004).

Malic enzyme (ME) has a high affinity for malate, and is only weakly inhibited by citrate, pyruvate, oxaloacetate, and ATP. ME is found in all lipogenic yeasts and its activity disappears following the period of active lipid accumulation. In contrast, acetyl-CoA carboxylase (ACC), fatty acid synthase (FAS), diacyglycerol acyltransferase (DGA), ATP:citrate lyase (ACL) and the NADPH-generating enzymes glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase and NADP(+):isocitrate dehydrogenase, do not demonstrate any changes in activities correlating with the accumulation of storage lipid (Wynn et al. 1999). ME therefore appears to be a source of NADPH for lipogenesis and a target for modification.

Metabolic pathways are often regulated at the first committing step. In this case, synthesis of malonyl-CoA, which is catalyzed by acetyl-CoA carboxylase (ACC), is a limiting step in attaining high titers of fatty acids and polyketides. Some versions of acetyl-CoA carboxylase are deactivated by a serine/threonine protein kinase, which is in turn activated by AMP. This relationship causes the acetyl-CoA carboxylase to be inactivated when glucose is depleted. To prevent this deactivation, a site-directed mutation is introduced in the serine residues of acetyl-CoA carboxylase that are phosphorylated by the AMP-activated protein kinase (AMPK). By converting these serines in Acct into an alanine or other non-serine and non-threonine residue, phosphorylation and inactivation is avoided. When the mutated gene is introduced into a host, acetyl-CoA carboxylase activity and total lipid accumulation increase.

Overexpression of the L. starkeyi ACC1 and GPD1 genes increase lipid production. Overexpression of ACC1, GUT2, and GUT1 also increases lipid production. In the case of GUT2 and GUT1 overexpression, higher levels of the coded proteins should increase the uptake of glycerol from thin stillage. In the case of ACC1 (acetyl-CoA carboxylase) overexpression and modification, altering the regulation should increase the formation of malonyl-CoA as a precursor for lipid synthesis and thereby increase the flux of malonyl-CoA into malonyl transferase which is an enzymatic activity of fatty acid synthase (FAS1).

Enzymes Involved in Substrate Assimilation

Lipomyces species and other lipogenic yeasts produce active amylases and other enzymes that degrade polysaccharides, and so are able to produce lipids from starch. L. starkeyi and other lipogenic yeasts also use a wide range of other polysaccharides (Gallagher et al. 1991, Punpeng et al. 1992, Steyn et al. 1995, Bignell et al. 2000, Ryu et al. 2000, Wilkie et al. 2000, Lee et al. 2003).

The genome of Lipomyces starkeyi contains numerous starch degrading alpha-amylase glycoside hydrolases (CAZY family GH13). Genes for several of these enzymes occur in clusters along with sugar transporters (e.g. Lipomyces starkeyi [PID_5034, PID_5035, PID_5036, PID_29016]; [PID_73677, PID_5097]; [PID_5097, PID_73677]; [PID_205534, PID_205437]; [PID_32360, PID_71673, PID_3625]). At least one of the alpha-amylases encoded in the L. starkeyi genome is thermostable (TAM1, PID_272826). Thermostable alpha-amylases are rarely found in yeasts. A gene for an amylo-alpha-1,6-glycosidase (dextranase) is also present (PID_5189) (Jeffries 2013). These features make L. starkeyi particularly suitable for lipid production when cultivated on starch (Gallagher et al. 1991, Punpeng et al. 1992).

Different strains of Lipomyces starkeyi show variable capacities for the assimilation of glycerol. The first step in glycerol metabolism is phosphorylation of glycerol by glycerol kinase (GUT1, PID_332345) to form glycerol-3-phosphate. This is followed by oxidation of glycerol-3-phosphate to dihydroxyacetone phosphate by an FAD-dependent glycerol-3-phosphate dehydrogenase (GUT2, PID_3942). Genes for both of these enzymes are present in Lipomyces starkeyi NRRL Y-11557 (Jeffries 2013).

Beta-1,4-endo-glucanase (BGL; GH5) depolymerizes glucan oligosaccharides. The genome of L. starkeyi encodes at least two GH5 cellulases, EGC1 and EGC2 (PID_72543 and PID_5513). The gene EGC1 is adjacent to a HXT2 sugar transporter (PID_4247) in the Lipomyces starkeyi genome. The HXT2 imports cellobiose (or cellulooligosaccharides). Beta-glucosidase (BGL; EC 3.2.1.21; GH3) is involved in the bioconversion of cellobiose to glucose. The genome of Lipomyces starkeyi encodes six putative enzymes in this family. At least one appears to be highly expressed (PID_69491) and at least two appear to be secreted (PID_147 and PID_5081). Several of the genes for GH3 proteins are proximally associated with genes coding for HXT2 sugar transporters (PID_3714, PID_334883, PID_7343).

Such proximal clustering of genes having associated physiological functions indicates that L. starkeyi has evolved for efficient use of beta- and alpha-linked glucans such as cellulose and starch.

The genome of L. starkeyi also contains a putative “glycoside hydrolase Family 61” auxiliary redox enzyme for cellulose hydrolysis (PID_61479) (Jeffries 2013). This protein includes a secretion signal and occurs rarely in ascomyceteous yeasts (Riley et al. 2016). This enzyme family is now known to not belong to the glycoside hydrolases, but rather is a “lytic polysaccharide mono-oxygenase” (LPMO). Enzymes belonging to this class are important components of commercial cellulase preparations (Cannella et al. 2014).

Glycerol kinase (GUT1) and glycerol-3-phosphate dehydrogenase (GUT2) are the first two genes involved in the assimilation of glycerol. Both of these genes are present in the genome of L. starkeyi NRRL-11557 (Jeffries 2013).

Any or all of the genes described above in L. starkeyi can be constitutively or overexpressed in L. starkeyi to enhance their activity therein.

Any or all of the genes described above in L. starkeyi can be incorporated in any other lipogenic yeast to confer similar benefits therein.

Genetic Targets for Metabolic Engineering

Various versions of the invention are directed to yeasts genetically modified to comprise one or more recombinant nucleic acids configured to express one or more proteins. The one or more recombinant nucleic acids are preferably configured to constitutively express or to overexpress the one or more proteins. The one or more recombinant nucleic acids preferably comprise one or more recombinant genes configured to constitutively express or to overexpress the one or more proteins. The expressed proteins include enzymes and other types of proteins such as transporters. If a cell endogenously expresses a particular protein, the nucleic acid expressing that protein may be modified to exchange or optimize promoters, exchange or optimize enhancers, or exchange or optimize any other genetic element that results in increased or constitutive expression of the proteins. Alternatively or additionally, one or more additional copies of a gene or coding sequence thereof may be introduced to the cell for enhanced expression of the proteins. If a cell does not endogenously express a particular protein, one or more copies of a recombinant nucleic acid configured to express that protein may be introduced to the cell for expression of the protein. The recombinant nucleic acid may be incorporated into the genome of the cell or may be contained on an extra-chromosomal plasmid. Techniques for genetic manipulation are described in further detail below. The genetically modified yeasts of the invention are also referred to herein as “recombinant,” “engineered,” or “bioengineered” yeasts, or other designations.

The recombinant yeasts of the invention may comprise one or more recombinant nucleic acids configured to express any one or more of the following proteins in any combination: an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme. The one or more recombinant nucleic acids preferably comprise one or more recombinant genes configured to express the above-referenced proteins.

For example, the recombinant yeasts of the invention may comprise one or more recombinant genes configured to express an acetyl-CoA carboxylase alone or with any one or more of an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express an alpha-amylase alone or with any one or more of an acetyl-CoA carboxylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express an ATP citrate lyase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a diacylglycerol acyltransferase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a fatty acid synthase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glycerol kinase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a 6-phosphogluconate dehydrogenase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glycerol-3-phosphate dehydrogenase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a malic enzyme alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a fatty acyl-CoA reductase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a delta-9 acyl-CoA desaturase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glycerol-3-phosphate acyltransferase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a lysophosphatidate acyltransferase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glucose-6-phosphate dehydrogenase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a beta-glucosidase alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a hexose transporter alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glycerol transporter alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express a glycoside hydrolase enzyme alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, and an auxiliary activity family 9 enzyme in any combination.

The recombinant yeasts of the invention may comprise one or more recombinant genes configured to express an auxiliary activity family 9 enzyme alone or with any one or more of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, and a glycoside hydrolase enzyme in any combination.

Acetyl-CoA carboxylases include enzymes falling under Enzyme Commission (EC) number 6.4.1.2. An exemplary acetyl-CoA carboxylase that may be expressed includes Acc1 (SEQ ID NO:2) encoded by Acc1 (SEQ ID NO:1) from L. starkeyi (PID_72701) Other exemplary acetyl-coA carboxylases include Acc1 mutants that comprise a residue other than serine at a position corresponding to position 1146 of SEQ ID NO:2. The residue at position 1146 is preferably a residue other than serine and threonine. The residue at position 1146 may be any amino acid other than serine or, more preferably any amino acid other than serine and threonine. The residue at position 1146 may be alanine. Other exemplary acetyl-coA carboxylases include Acc1 mutants that comprise serine at a position corresponding to position 639 of SEQ ID NO:2 and a residue other than serine and threonine at a position corresponding to position 1146 of SEQ ID NO:2.

Alpha-amylases include enzymes falling under EC number 3.2.1.1. Exemplary alpha-amylases that may be expressed include the secreted alpha-amylase designated by PID_3772 (SEQ ID NO:4) encoded by the corresponding nucleic acid (SEQ ID NO:3) from Lipomyces starkeyi, the thermostable α-amylase designated by PID_272826 (SEQ ID NO:6) encoded by the corresponding nucleic acid (SEQ ID NO:5) from L. starkeyi, and a chimera of the secreted alpha-amylase and the thermostable α-amylase (SEQ ID NO:8) encoded by the corresponding nucleic acid (SEQ ID NO:7).

ATP citrate lyases include enzymes falling under EC number 2.3.3.8. An exemplary ATP citrate lyase that may be expressed includes the alpha subunit Acl1 (SEQ ID NO:10) encoded by Acl1 (SEQ ID NO:9) and the beta subunit Acl2 (SEQ ID NO:12) encoded by Acl2 (SEQ ID NO:11) from L. starkeyi. The alpha and beta subunits are preferably expressed as a pair.

Diacylglycerol acyltransferases (DGAs) include enzymes falling under EC number 2.3.1.20. Exemplary diacylglycerol acyltransferases that may be expressed include a 1233 variant of DGA1 (SEQ ID NO:14) encoded by DGA1-1233 (SEQ ID NO:13), a 1389 variant of DGA1 (SEQ ID NO:16) encoded by DGA1-1389 (SEQ ID NO:15), and DGA2 (SEQ ID NO:58) encoded by DGA2 (SEQ ID NO:57), all derived from L. starkeyi. The 1233 variant of DGA1 is identical to the 1389 variant except that it lacks the first 52 residues of the 1389 variant. The 1233 variant unexpectedly confers enhanced lipogenic properties compared to the 1389 variant. Accordingly, preferred diacylglycerol acyltransferases of the invention lack a sequence corresponding to positions 1-52 of SEQ ID NO:16.

Fatty acid synthases (FASs) include enzymes falling under EC number 2.3.1.85. Exemplary fatty acid synthases that may be expressed include any combination of alpha and beta fatty acid synthase subunits from L. starkeyi. Alpha fatty acid synthase subunits from L. starkeyi include FAS2.1 (SEQ ID NO:18) encoded by FAS2.1 (SEQ ID NO:17) and FAS2.2 (SEQ ID NO:22) encoded by FAS2.2 (SEQ ID NO:21). Beta fatty acid synthase subunits from L. starkeyi include FAS1.1 (SEQ ID NO:20) encoded by FAS1.1 (SEQ ID NO:19) and FAS1.2 (SEQ ID NO:24) encoded by FAS1.2 (SEQ ID NO:23). FAS2.1 is preferably expressed with FAS1.1, and FAS2.2 is preferably expressed with FAS1.2. However, FAS2.1 may be expressed with FAS1.2, and FAS2.2 may be expressed with FAS1.1.

Glycerol kinases include enzymes falling under EC number 2.7.1.30. Exemplary glycerol kinases that may be expressed include a 1602 variant of GUT1 (SEQ ID NO:26) encoded by GUT1-1602 (SEQ ID NO:25) and a 1617 variant of GUT1 (SEQ ID NO:28) encoded by GUT1-1617 (SEQ ID NO:27), both derived from L. starkeyi. The 1602 variant of DGA1 is identical to the 1617 variant except that it lacks the first 5 residues of the 1617 variant. Accordingly, some glycerol kinases of the invention lack a sequence corresponding to positions 1-5 of SEQ ID NO:28.

6-Phosphogluconate dehydrogenases include enzymes falling under EC number 1.1.1.44. An exemplary 6-phosphogluconate dehydrogenase that may be expressed includes GND1 (SEQ ID NO:30) encoded by GND1 (SEQ ID NO:29) from L. starkeyi.

Glycerol-3-phosphate dehydrogenases include enzymes falling under EC number 1.1.1.8. Exemplary glycerol-3-phosphate dehydrogenases that may be expressed include GPD1 (SEQ ID NO:32) encoded by GPD1 (SEQ ID NO:31) and the FAD-dependent glycerol-3-phosphate dehydrogenase GUT2 (SEQ ID NO:56) encoded by GUT2 (SEQ ID NO:55), both from L. starkeyi.

Malic enzymes include enzymes falling under EC numbers 1.1.1.38, 1.1.1.39, 1.1.1.40, and 83. An exemplary malic enzyme that may be expressed includes ME (SEQ ID NO:34) encoded by ME (SEQ ID NO:33) from L. starkeyi.

Fatty acyl-CoA reductases include enzymes falling under EC numbers 1.2.1, such as 1.2.1.84 and others. These enzymes include the preferred alcohol-forming fatty acyl-CoA reductases (EC 1.2.1.84). An exemplary fatty acyl-CoA reductase that may be expressed includes FALDR (SEQ ID NO:36) encoded by FALDR (SEQ ID NO:35) from Marinobacter aquaeolei.

Delta-9 acyl-CoA desaturases include enzymes falling under EC number 1.14.19.1. An exemplary delta-9 acyl-CoA desaturase that may be expressed includes OLE1 (SEQ ID NO:38) encoded by OLE1 (SEQ ID NO:37) from L. starkeyi. In addition to or instead of expressing a delta-9 acyl-CoA desaturase, other fatty acid desaturases may be expressed, such as acyl-CoA (8-3)-desaturases (delta-5 desaturases) (EC 1.14.19.44) and acyl-CoA 6-desaturases (delta-6 desaturases) (EC 1.14.19.3).

Glycerol-3-phosphate acyltransferases include enzymes falling under EC number 2.3.1.15. An exemplary glycerol-3-phosphate acyltransferase that may be expressed includes SCT1 (SEQ ID NO:40) encoded by SCT1 (SEQ ID NO:39) from L. starkeyi.

Lysophosphatidate acyltransferases include enzymes falling under EC number 2.3.1.51. An exemplary lysophosphatidate acyltransferase that may be expressed includes SLC1 (SEQ ID NO:42) encoded by SLC1 (SEQ ID NO:41) from L. starkeyi.

Glucose-6-phosphate dehydrogenases include enzymes falling under EC number 1.1.1.49. An exemplary glucose-6-phosphate dehydrogenase that may be expressed includes ZWF1 (SEQ ID NO:44) encoded by ZWF1 (SEQ ID NO:43) from L. starkeyi.

Beta-glucosidases include enzymes falling under EC number 3.2.1.21. An exemplary beta-glucosidase that may be expressed includes BGL1.1 (SEQ ID NO:46) encoded by BGL1.1 (SEQ ID NO:45) from L. starkeyi.

Hexose transporters include proteins falling under the Hxt family (e.g., Hxt1, Hxt2, Hxt3, Hxt4, Hxt5, Hxt6, Hxt7, Hxt8, Hxt9, Hxt11, etc.). An exemplary hexose transporter that may be expressed includes Hxt2.2 (SEQ ID NO:48) encoded by Hxt2.2 (SEQ ID NO:47) from L. starkeyi.

Glycerol transporters that may be expressed include the glycerol/H+symporters STL1 (SEQ ID NO:64) encoded by STL1 (SEQ ID NO:63) and STL2 (SEQ ID NO:66) encoded by STL2 (SEQ ID NO:65) from L. starkeyi. Glycerol transporters that may be expressed also include the glycerol facilitator FPS1 (SEQ ID NO:68) encoded by FPS1 (SEQ ID NO:67) from L. starkeyi.

Glycoside hydrolases include a number of families. Preferred glycoside hydrolases that may be expressed include glycoside hydrolase family 5 enzymes. Glycoside hydrolase family 5 enzymes include endoglucanases (EC 3.2.1.4), beta-mannanases (EC 3.2.1.78), exo-1,3-glucanases (EC 3.2.1.58), endo-1,6-glucanases (EC 3.2.1.75), xylanases (EC 3.2.1.8), endoglycoceramidases (EC 3.2.1.123), and trehalases (EC 3.2.1.28). Preferred glucosidase hydrolase family 5 enzymes that may be expressed include endoglucanases. Exemplary endoglucanases that may be expressed include EGC1 (SEQ ID NO:50) encoded by EGC1 (SEQ ID NO:49) from L. starkeyi and EGC2 (SEQ ID NO:52) encoded by EGC2 (SEQ ID NO:51) from L. starkeyi. Exemplary trehalases that may be expressed include the “neutral” trehalase NTH1 (SEQ ID NO:60) encoded by NTH1 (SEQ ID NO:59) and the “acidic” trehalase ATH1 (SEQ ID NO:62) encoded by ATH1 (SEQ ID NO:61), both from L. starkeyi.

Auxiliary activity family 9 enzymes are copper-dependent lytic polysaccharide monooxygenases (LPMOs). These enzymes are involved in the cleavage of cellulose chains with oxidation of various carbons (C-1, C-4 and C-6). Auxiliary activity family 9 enzymes were originally classified as glycoside hydrolases under glycoside hydrolase family 61 (GH61). An exemplary auxiliary activity family 9 enzyme that may be expressed includes AAC9 (SEQ ID NO:54) encoded by AAC9 (SEQ ID NO:53) from L. starkeyi.

Other suitable proteins that may be expressed include those comprising polypeptide sequences at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical to the sequences listed above. Other suitable proteins that may be expressed include orthologs and paralogs of the proteins listed above. Other suitable proteins that may be expressed include those comprising polypeptide sequences at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical to orthologs and paralogs of the proteins listed above. The orthologs are preferably from lipogenic yeasts, such as any of the lipogenic yeasts described herein. The recombinant gene encoding the proteins may include introns or be devoid of introns or any or all other non-coding regions in the native gene. Any nucleotide sequences capable of expressing the polypeptide sequences encompassed herein are acceptable. Tremendous variation from the exemplary nucleotide sequences described herein is possible due to the redundancy in the genetic code and codon optimization.

Coding sequences of the above-mentioned proteins are preferably operably linked to a promoter. The promoter may be a constitutive promoter or an inducible promoter. Exemplary promoters that may be operably linked to the coding sequences of the above-mentioned proteins include the L. starkeyi ATPase 3900 promoter (SEQ ID NO:75), the L. starkeyi citrate synthase (CIT1) promoter (SEQ ID NO:76), the L. starkeyi fructose bisphosphate aldolase (FBA1) promoter (SEQ ID NO:77), the L. starkeyi glutamine synthetase (GLN1) promoter (SEQ ID NO:78), the L. starkeyi glyceraldehyde 3-phosphate dehydrogenase (TDH3) promoter (SEQ ID NO:79), the L. starkeyi pyruvate kinase (PYK1) promoter (SEQ ID NO:80), the L. starkeyi translation elongation factor (TEF1) promoter (SEQ ID NO:81), the L. starkeyi triosephosphate isomerase (TPI) promoter (SEQ ID NO:82), the L. starkeyi enolase (ENO1) promoter (SEQ ID NO:83), the copper inducible (CUP1) promoter (SEQ ID NO:84), or sequence variants at least about at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical thereto.

Coding sequences of the above-mentioned proteins are preferably operably linked to a terminator. Exemplary terminators that may be operably linked to the coding sequences of the above-mentioned proteins include the L. starkeyi ATPase 3900 terminator (SEQ ID NO:85), the L. starkeyi fructose bisphosphate aldolase (FBA1) terminator (SEQ ID NO:86), the L. starkeyi glutamine synthetase (GLN1) terminator (SEQ ID NO:87), the L. starkeyi glyceraldehyde 3-phosphate dehydrogenase (TDH3) terminator (SEQ ID NO:88), the L. starkeyi pyruvate kinase (PYK1) terminator (SEQ ID NO:89), the L. starkeyi triosephosphate isomerase (TPI) terminator (SEQ ID NO:90), or sequence variants at least about at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical thereto.

In addition to expressing any one or more of the proteins listed above, the recombinant yeasts of the invention may be modified to reduce or ablate the activity of one or more native or non-native proteins. The recombinant yeasts, for example, may comprise a modification that reduces or ablates the activity of one or more of the following native proteins: a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate dehydrogenase, an acyl-CoA oxidase, a 3-hydroxyacyl-CoA dehydrogenase, and an enoyl-CoA hydratase.

Delta-9 acyl-CoA desaturases include enzymes falling under EC number 1.14.19.1. An exemplary delta-9 acyl-CoA desaturase whose activity may be reduced or ablated includes OLE1 (SEQ ID NO:38) encoded by OLE1 (SEQ ID NO:37) from L. starkeyi. In addition to or instead of reducing or ablating the activity of a delta-9 acyl-CoA desaturase, the activity of other fatty acid desaturases may be reduced or ablated, such as acyl-CoA (8-3)-desaturases (delta-5 desaturases) (EC 1.14.19.44) and acyl-CoA 6-desaturases (delta-6 desaturases) (EC 1.14.19.3).

Glycerol-3-phosphate dehydrogenases include enzymes falling under EC number 1.1.1.8. An exemplary glycerol-3-phosphate dehydrogenase whose activity may be reduced or ablated includes the FAD-dependent glycerol-3-phosphate dehydrogenase GUT2 (SEQ ID NO:56) encoded by GUT2 (SEQ ID NO:55) from L. starkeyi.

Acyl-CoA oxidases include enzymes falling under EC number 1.3.3.6. An exemplary acyl-CoA oxidase whose activity may be reduced or ablated includes PDX1 (SEQ ID NO:70) encoded by PDX1 (SEQ ID NO:69) from L. starkeyi. Acyl-CoA oxidases catalyze the first step of beta oxidation.

Enoyl-CoA hydratases include enzymes falling under EC number 4.2.1.17. An exemplary enoyl-CoA hydratase whose activity may be reduced or ablated includes FOX1 (SEQ ID NO:72) encoded by FOX1 (SEQ ID NO:71) from L. starkeyi. Enoyl-CoA hydratases catalyze the third step of beta oxidation.

3-Hydroxyacyl-CoA dehydrogenases include enzymes falling under EC number 1.1.1.35. An exemplary 3-hydroxyacyl-CoA dehydrogenase whose activity may be reduced or ablated includes FOX1 (SEQ ID NO:72) encoded by FOX1 (SEQ ID NO:71) from L. starkeyi. 3-hydroxyacyl-CoA dehydrogenases catalyze the second step of beta oxidation.

Certain enzymes are multifunctional and have more than one enzymatic activity. Examples include the FOX1 (SEQ ID NO:72) encoded by FOX1 (SEQ ID NO:71) from L. starkeyi, which has both 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase activities, and is thereby considered to be both a 3-hydroxyacyl-CoA dehydrogenase and an enoyl-CoA hydratase.

Other suitable proteins whose activity may be reduced or ablated include those comprising amino acid sequences at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical to the sequences listed above. Other suitable proteins whose activity may be reduced or ablated include orthologs and paralogs of the proteins listed above. Other suitable proteins whose activity may be reduced or ablated include those comprising amino acid sequences at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, or at least about 99% identical to orthologs and paralogs of the proteins listed above.

A modification that reduces or ablates the activity of a gene product such as a protein is referred to herein as a “functional deletion.” “Functional deletion” or its grammatical equivalents refers to any modification to a microorganism that ablates, reduces, inhibits, or otherwise disrupts production of a gene product, renders a produced gene product non-functional, or otherwise reduces or ablates a produced gene product's activity. Accordingly, in some instances, a gene product that is functionally deleted means that the gene product is not produced by the microorganism at all. “Gene product” refers to a protein or polypeptide encoded and produced by a particular gene. “Gene” refers to a nucleic acid sequence capable of producing a gene product and may include such genetic elements as a coding sequence together with any other genetic elements required for transcription and/or translation of the coding sequence. Such genetic elements may include a promoter, an enhancer, and/or a ribosome binding site (RBS), among others.

One of ordinary skill in the art will appreciate that there are many well-known ways to functionally delete a gene product. For example, functional deletion can be accomplished by introducing one or more genetic modifications. As used herein, “genetic modifications” refer to any differences in the nucleic acid composition of a cell, whether in the cell's native chromosome or in endogenous or exogenous non-chromosomal plasmids harbored within the cell. Examples of genetic modifications that may result in a functionally deleted gene product include but are not limited to substitutions, partial or complete deletions, insertions, or other variations to a coding sequence or a sequence controlling the transcription or translation of a coding sequence, such as placing a coding sequence under the control of a less active promoter, etc. In some versions, a gene or coding sequence can be replaced with a selection marker or screenable marker. Various methods for introducing genetic modifications are well known in the art and include homologous recombination, among other mechanisms. See, e.g., Green et al., Molecular Cloning: A laboratory manual, 4^(th) ed., Cold Spring Harbor Laboratory Press (2012) and Sambrook et al., Molecular Cloning: A Laboratory Manual, 3^(rd) ed., Cold Spring Harbor Laboratory Press (2001). In some versions, functional deletion can be accomplished by expressing ribozymes or antisense sequences that target the mRNA of the gene of interest. Functional deletion can also be accomplished by inhibiting the activity of the gene product, for example, by chemically inhibiting a gene product with a small-molecule inhibitor, by expressing a protein that interferes with the activity of the gene product, or by other means. In some versions, the functional deletion may comprise an activity-reducing or activity-ablating mutation in the endogenous gene. The activity-reducing or activity-ablating mutation in the endogenous gene may comprise a nucleotide substitution in the endogenous gene, a nucleotide insertion in the endogenous gene, a partial deletion of the endogenous gene, and/or a complete deletion of the endogenous gene.

In certain versions of the invention, the functionally deleted gene product may have less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the activity of the non-functionally deleted gene product.

In certain versions of the invention, a cell with a functionally deleted gene product may have less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the activity of the gene product compared to a cell with the non-functionally deleted gene product.

In certain versions of the invention, the functionally deleted gene product may be expressed at an amount less than about 95%, less than about 90%, less than about 85%, less than about 80%, less than about 75%, less than about 70%, less than about 65%, less than about 60%, less than about 55%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 1%, or about 0% of the amount of the non-functionally deleted gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, or more nonsynonymous substitutions are present in the gene or coding sequence of the gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least 1, at least 2, at least 3, at least 4, at least 5, at least 10, at least 20, at least 30, at least 40, at least 50, or more bases are inserted in the gene or coding sequence of the gene product.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of the gene product's gene or coding sequence is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of a promoter driving expression of the gene product is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of an enhancer controlling transcription of the gene product's gene is deleted or mutated.

In certain versions of the invention, the functionally deleted gene product may result from a genetic modification in which at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% of a sequence controlling translation of the gene product's mRNA is deleted or mutated.

In certain versions of the invention, the decreased activity or expression of the functionally deleted gene product is determined with respect to the activity or expression of the gene product in its unaltered state as found in nature. In certain versions of the invention, the decreased activity or expression of the functionally deleted gene product is determined with respect to the activity or expression of the gene product in its form in a corresponding microorganism. In certain versions, the genetic modifications giving rise to a functionally deleted gene product are determined with respect to the gene in its unaltered state as found in nature. In certain versions, the genetic modifications giving rise to a functionally deleted gene product are determined with respect to the gene in its form in a corresponding microorganism. As used herein, “corresponding microorganism” refers to a microorganism of the same species having the same or substantially same genetic and proteomic composition as a microorganism of the invention, with the exception of genetic and proteomic differences resulting from the manipulations described herein for the microorganisms of the invention.

The yeasts of the invention with the modifications described herein preferably exhibit a property selected from the group consisting of increased lipid production, increased lipid secretion, increased lipid production under nitrogen-rich conditions, increased lipid yield, increased lipid secretion under nitrogen-rich conditions, increased enzyme production, increased enzyme secretion, increased carbohydrase production, increased carbohydrase secretion, increased growth rates, and/or increased organic consumption, such as increased glycerol consumption and/or and increased disaccharide (cellobiose and/or trehalose) consumption relative to a non-recombinant control. “Carbohydrase” refers to any enzyme capable of breaking down a carbohydrate, such as amylases, cellulases, glucosidases, etc.

Nitrogen-rich conditions exist when the form, the amount, or form and amount of nitrogen biologically available to the cell exceeds the amount of carbon source necessary for balanced cell growth. The form of nitrogen refers to the chemical form in which it is supplied to the cells. An easily assimilated nitrogen source includes amino acids or extracts of yeast cells. These nitrogen sources require less metabolic energy for assimilation and provide carbon at the same time. A less readily assimilated nitrogen source includes inorganic salts of ammonium or nitrate or nitrogen supplied as urea. Elemental nitrogen or nitrogen bound in insoluble minerals are not generally considered biologically available to fungi. Nitrogen-rich conditions can exist when either readily assimilated or less-readily assimilated nitrogen sources are provided to a cell in excess of the amount of carbon required for protein, nucleic acid and cell wall synthesis.

Nitrogen-poor conditions can exist when the amount of readily available or less readily available nitrogen supplied is substantially less than the amount of available carbon source that can be assimilated. A nitrogen-poor or nitrogen-limiting condition could also exist when an easily assimilated nitrogen source is supplied slowly or in a slow-release formulation.

As in the case of the nitrogen supply, the carbon source can be readily assimilated, less readily assimilated, poorly assimilated or not assimilated. The cell can use readily assimilated carbon source such as glucose to rapidly generate metabolic energy. A carbon source such as glycerol, cellobiose or other oligosaccharides might or might not be readily assimilated depending on the enzymes available for its metabolism and the conditions of growth such as the supply of oxygen.

A nitrogen-rich condition in a native organism can be identified as a concentration above a nitrogen-limited concentration, wherein the nitrogen-limited concentration includes all concentrations at or below the concentration of nitrogen in which any decreases thereof increase the amount of lipid produced and/or accumulated by the organism.

Acetyl-CoA carboxylase and diacylglycerol acyltransferase are both preferred targets for increasing lipid production. Overexpression of acetyl-CoA carboxylase results in increased rates of fatty acid biosynthesis and fatty acid content. The Acct acetyl-CoA carboxylase of L. starkeyi has serine residues at positions corresponding to 639 and 1146 of SEQ ID NO2. The inventors have determined that the serine at position 1146 is responsible for downregulating ACC1 activity upon post-translational modification. Certain versions of this invention modify the serine at position 1146 to an amino acid other than serine or threonine, such as alanine or any other amino acid, to prevent this downregulation.

Overexpression of diacylglycerol acyltransferase leads to an increase in lipid production. This lipid production is increased even further following overexpression of acetyl-CoA carboxylase. The present inventors surmise that a sink for triglyceride synthesis, such as through high expression of diacylglycerol acyltransferase, should be present in order for overexpression of acetyl-CoA carboxylase to be fully effective.

One of the prerequisites of oleaginous organisms is the ability to produce a continuous supply of acetyl-CoA precursors in the cytosol. ATP citrate lyase acts as the primary source of cytosolic acetyl-CoA in these species, and is believed to be one of the rate limiting steps of lipid biosynthesis. The activity of ATP citrate lyase correlates well with the specific rate of lipid biosynthesis in L. starkeyi. In Lipomyces both intracellular and extracellular citrate levels rise in response to nitrogen limitation (Holdsworth et al. 1988). Citrate accumulation may represent a bottleneck, which could be overcome by increasing ATP citrate lyase activity in the cytosol or citrate synthase (CS) in the mitochondria.

NADPH, which is required for lipid biosynthesis, is largely supplied by the oxidative pentose phosphate pathway (PPP). Native lipogenic yeasts possess a highly active oxidative pentose phosphate pathway along with an enzyme system that exports citric acid to the cytosol where it is converted into acetyl-CoA and NADPH that feed into lipid synthesis. Modification of lipogenic enzymes or alteration of gene expression that boosts these systems can further increase lipid synthesis in native lipogenic yeasts. Overexpression of 6-phosphogluconate dehydrogenase (GND1) and/or glucose-6-phosphate dehydrogenase (ZWF1), for example, are predicted to increase the supply of NADPH for lipid synthesis, but since ZWF1 and (particularly) GND1 are subject to strong allosteric regulation by physiological levels of NADPH (Barcia-Vieitez et al. 2014, Rippa et al. 1998, Velasco et al. 1995), modification of the regulatory controls are predicted to be more effective. For example, substitution of the tyrosine at position 99 (i.e., Y99) of the ZWF1 of L. starkeyi represented by SEQ ID NO:44 can alter binding of NADPH and thereby render this enzyme resistant to allosteric regulation by NADPH. The tyrosine in ZWF1 can be substituted by any amino acid. The tyrosine in ZWF1 is preferably substituted with serine, threonine, glutamine asparagine, cysteine, alanine, proline, leucine, isoleucine, phenylalanine, valine, histidine, lysine, asparagine, aspartic, glutamic acid, or glycine; more preferably substituted with serine or threonine; and most preferably substituted with serine. An analogous substitution in GND1 can also or alternatively be performed to render GND1 resistant to allosteric regulation by NADPH.

The NADPH supplied by malic enzyme has a strong influence on lipid accumulation in lipogenic yeasts. Increasing malic enzyme activity is predicted to provide lipogenic yeasts with more NADPH for lipid synthesis.

Another approach to increasing the production of lipid is to reduce activity of the β-oxidation pathway. The β-oxidation pathway is responsible for consuming lipid after lipogenic yeasts exhaust their carbohydrate sources Eliminating the breakdown of lipids is therefore another target for developing yeasts with enhanced lipid production. Exemplary modifications in this regard include functional deletion of an acyl-CoA oxidase, a 3-hydroxyacyl-CoA dehydrogenase, and/or an enoyl-CoA hydratase. Acyl-CoA oxidases catalyze the first step in beta oxidation. Enoyl-CoA hydratases catalyze the second step in beta oxidation. 3-Hydroxyacyl-CoA dehydrogenases catalyze the third step in beta oxidation. PDX1 is an exemplary acyl-CoA oxidase in L. starkeyi. FOX1 is a multifunctional enzyme in L. starkeyi that can be considered to be both a 3-hydroxyacyl-CoA dehydrogenase and an enoyl-CoA hydratase, as it has both 3-hydroxyacyl-CoA dehydrogenase and enoyl-CoA hydratase activities. Other modifications that inhibit lipid oxidation are acceptable.

Disruption of the gene for the regulatory protein CreA/Mig 1 in Y lipolytica increased the lipid content from 36% to 48.7% of its dry weight while increasing the C_(18:1) content (Wang et al. 2013). A CreA homolog in the L. starkeyi genome is similar to the CreA transcriptional activator of Y lipolytica, and could be a good target to determine whether disruption of the CREA/MIG1 homolog in L. starkeyi results in an increase in lipid production.

For Mucor circinelloides (Zhang et al. 2008), Rhodotorula glutinis (Li et al. 2012), and Yarrowia lipolytica (Tai et al. 2013), the basal lipid production contents of the parental strains are all considerably lower than what has been observed in native (non-engineered) L. starkeyi under nitrogen limiting conditions (≈65%), indicating that there is substantial room for improvement in these strains with the modifications described herein.

Genetic Engineering

The cells of the invention may be genetically altered to functionally delete, express, or overexpress any of the specific genes or gene products explicitly described herein or homologs thereof. Proteins and/or protein sequences are “homologous” when they are derived, naturally or artificially, from a common ancestral protein or protein sequence. Similarly, nucleic acids and/or nucleic acid sequences are homologous when they are derived, naturally or artificially, from a common ancestral nucleic acid or nucleic acid sequence. Nucleic acid or gene product (amino acid) sequences of any known gene, including the genes or gene products described herein, can be determined by searching any sequence databases known in the art using the gene name or accession number as a search term. Common sequence databases include GenBank (www.ncbi.nlm.nih.gov), ExPASy (expasy.org), KEGG (www.genome.jp), among others. Homology is generally inferred from sequence similarity between two or more nucleic acids or proteins (or sequences thereof). The precise percentage of similarity between sequences that is useful in establishing homology varies with the nucleic acid and protein at issue, but as little as 25% sequence similarity (e.g., identity) over 50, 100, 150 or more residues (nucleotides or amino acids) is routinely used to establish homology (e.g., over the full length of the two sequences to be compared). Higher levels of sequence similarity (e.g., identity), e.g., 30%, 35% 40%, 45% 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% or more, can also be used to establish homology. Accordingly, homologs of the genes or gene products described herein include genes or gene products having at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% identity to the genes or gene products described herein. Methods for determining sequence similarity percentages (e.g., BLASTP and BLASTN using default parameters) are described herein and are generally available. The homologous proteins should demonstrate comparable activities and, if an enzyme, participate in the same or analogous pathways. Homologs include orthologs and paralogs. “Orthologs” are genes and products thereof in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same or similar function in the course of evolution. Paralogs are genes and products thereof related by duplication within a genome. As used herein, “orthologs” and “paralogs” are included in the term “homologs.”

For sequence comparison and homology determination, one sequence typically acts as a reference sequence to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are input into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. The sequence comparison algorithm then calculates the percent sequence identity for the test sequence(s) relative to the reference sequence based on the designated program parameters. A typical reference sequence of the invention is a nucleic acid or amino acid sequence corresponding to the genes or gene products described herein.

Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by visual inspection (see Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (supplemented through 2008)).

One example of an algorithm that is suitable for determining percent sequence identity and sequence similarity for purposes of defining homologs is the BLAST algorithm, which is described in Altschul et al., J. Mol. Biol. 215:403-410 (1990). Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always>0) and N (penalty score for mismatching residues; always<0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl. Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Natl. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001. The above-described techniques are useful in identifying homologous sequences for use in the methods described herein.

The terms “identical” or “percent identity”, in the context of two or more nucleic acid or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described above (or other algorithms available to persons of skill) or by visual inspection.

The phrase “substantially identical” in the context of two nucleic acids or polypeptides refers to two or more sequences or subsequences that have at least about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90, about 95%, about 98%, or about 99% or more nucleotide or amino acid residue identity, when compared and aligned for maximum correspondence, as measured using a sequence comparison algorithm or by visual inspection. Such “substantially identical” sequences are typically considered to be “homologous”, without reference to actual ancestry. Preferably, the “substantial identity” exists over a region of the sequences that is at least about 50 residues in length, more preferably over a region of at least about 100 residues, and most preferably, the sequences are substantially identical over at least about 150 residues, at least about 250 residues, or over the full length of the two sequences to be compared.

Terms used herein pertaining to genetic manipulation are defined as follows.

Deletion: The removal of one or more nucleotides from a nucleic acid molecule or one or more amino acids from a protein, the regions on either side being joined together.

Derived: When used with reference to a nucleic acid or protein, “derived” means that the nucleic acid or polypeptide is isolated from a described source or is at least 70%, 80%, 90%, 95%, 99%, or more identical to a nucleic acid or polypeptide included in the described source.

Endogenous: As used herein with reference to a nucleic acid molecule, genetic element (e.g., gene, promoter, etc.), or polypeptide in a particular cell, “endogenous” refers to a nucleic acid molecule, genetic element, or polypeptide that is in the cell and was not introduced into the cell or transferred within the genome of the cell using recombinant engineering techniques. For example, an endogenous genetic element is a genetic element that was present in a cell in its particular locus in the genome when the cell was originally isolated from nature. The term “native” is used herein interchangeably with “endogenous.”

Exogenous: As used herein with reference to a nucleic acid molecule, genetic element (e.g., gene, promoter, etc.), or polypeptide in a particular cell, “exogenous” refers to any nucleic acid molecule, genetic element, or polypeptide that was introduced into the cell or transferred within the genome of the cell using recombinant engineering techniques. For example, an exogenous genetic element is a genetic element that was not present in its particular locus in the genome when the cell was originally isolated from nature. The term “heterologous” is used herein interchangeably with “exogenous.”

Expression: The process by which a gene's coded information is converted into the structures and functions of a cell, such as a protein, transfer RNA, or ribosomal RNA. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein (for example, transfer and ribosomal RNAs).

Introduce: When used with reference to genetic material, such as a nucleic acid, and a cell, “introduce” refers to the delivery of the genetic material to the cell in a manner such that the genetic material is capable of being expressed within the cell. Introduction of genetic material includes both transformation and transfection. Transformation encompasses techniques by which a nucleic acid molecule can be introduced into cells such as prokaryotic cells or non-animal eukaryotic cells. Transfection encompasses techniques by which a nucleic acid molecule can be introduced into cells such as animal cells. These techniques include but are not limited to introduction of a nucleic acid via conjugation, electroporation, lipofection, infection, and particle gun acceleration.

Isolated: An “isolated” biological component (such as a nucleic acid molecule, polypeptide, or cell) has been substantially separated or purified away from other biological components in which the component naturally occurs, such as other chromosomal and extrachromosomal DNA and RNA and proteins. Nucleic acid molecules and polypeptides that have been “isolated” include nucleic acid molecules and polypeptides purified by standard purification methods. The term also includes nucleic acid molecules and polypeptides prepared by recombinant expression in a cell as well as chemically synthesized nucleic acid molecules and polypeptides. In one example, “isolated” refers to a naturally-occurring nucleic acid molecule that is not immediately contiguous with both of the sequences with which it is immediately contiguous (one on the 5′ end and one on the 3′ end) in the naturally-occurring genome of the organism from which it is derived.

Nucleic acid: Encompasses both RNA and DNA molecules including, without limitation, cDNA, genomic DNA, and mRNA. Nucleic acids also include synthetic nucleic acid molecules, such as those that are chemically synthesized or recombinantly produced. The nucleic acid can be double-stranded or single-stranded. Where single-stranded, the nucleic acid molecule can be the sense strand, the antisense strand, or both. In addition, the nucleic acid can be circular or linear.

Operably linked: A first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. An origin of replication is operably linked to a coding sequence if the origin of replication controls the replication or copy number of the nucleic acid in the cell. Operably linked nucleic acids may or may not be contiguous.

Operon: Configurations of separate genes that are transcribed in tandem as a single messenger RNA are denoted as operons. Thus, a set of in-frame genes in close proximity under the transcriptional regulation of a single promoter constitutes an operon. Operons may be synthetically generated using the methods described herein.

Overexpress: When a gene is caused to be transcribed at an elevated rate compared to the endogenous or basal transcription rate for that gene. In some examples, overexpression additionally includes an elevated rate of translation of the gene compared to the endogenous translation rate for that gene. Methods of testing for overexpression are well known in the art, for example transcribed RNA levels can be assessed using RT-PCR and protein levels can be assessed using SDS-PAGE gel analysis.

Recombinant: A recombinant nucleic acid molecule, genetic element (e.g., gene, promoter, etc.), or polypeptide is one that has a sequence that is not naturally occurring, is present in a different locus (e.g., genetic locus or on an extrachromosomal plasmid) within a particular cell than in a corresponding native cell, or both. A recombinant cell or microorganism is one that contains a recombinant nucleic acid molecule, genetic element, or polypeptide.

Vector or expression vector: An entity comprising a nucleic acid molecule that is capable of introducing the nucleic acid, or being introduced with the nucleic acid, into a cell for expression of the nucleic acid. A vector can include nucleic acid sequences that permit it to replicate in the cell, such as an origin of replication. A vector can also include one or more selectable marker genes and other genetic elements known in the art. Examples of suitable vectors are found below.

Unless explained otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, suitable methods and materials are described below.

Exogenous nucleic acids can be introduced stably or transiently into a cell using techniques well known in the art, including electroporation, lithium acetate transformation, calcium phosphate precipitation, DEAE-dextran mediated transfection, liposome-mediated transfection, conjugation, transduction, and the like. For stable transformation, a nucleic acid can further include a selectable marker. Suitable selectable markers include antibiotic resistance genes that confer, for example, resistance to nourseothricin, G418, hygromycin B, neomycin, tetracycline, chloramphenicol, or kanamycin, genes that complement auxotrophic deficiencies, and the like. (See below for more detail.)

Various embodiments of the invention use an expression vector that includes a recombinant nucleic acid encoding a protein involved in a metabolic or biosynthetic pathway. Suitable expression vectors include, but are not limited to viral vectors, phage vectors, bacteriophage vectors, plasmids, phagemids, cosmids, fosmids, bacterial artificial chromosomes, Pl-based artificial chromosomes, yeast plasmids, yeast artificial chromosomes, and any other vectors specific for cells of interest.

Useful vectors can include one or more selectable marker genes to provide a phenotypic trait for selection of transformed cells. The selectable marker gene encodes a protein necessary for the survival or growth of transformed cells grown in a selective culture medium. Cells not transformed with the vector containing the selectable marker gene will not survive in the culture medium. Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., nourseothricin, G418, hygromycin B, ampicillin, neomycin, methotrexate, or tetracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media. In alternative embodiments, the selectable marker gene is one that encodes orotidine 5′-phosphate decarboxylase, dihydrofolate reductase or confers neomycin resistance (for use in eukaryotic cell culture).

The coding sequence in the expression vector is operably linked to an appropriate expression control sequence (promoters, enhancers, and the like) to direct synthesis of the encoded gene product. Such promoters can be derived from endogenous or exogenous sources. Thus, the recombinant genes of the invention can comprise a coding sequence operably linked to a heterologous genetic element, such as a promoter, enhancer, ribosome binding site, etc. “Heterologous” in this context refers to a genetic element that is not operably linked to the coding sequence in nature. Depending on the cell/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. can be used in the expression vector (see e.g., Bitter et al. (1987) Methods in Enzymology, 153:516-544).

Non-limiting examples of suitable promoters for use within a eukaryotic cell are typically viral in origin and include the promoter of the mouse metallothionein I gene (Hamer et al. (1982) J. Mol. Appl. Gen. 1:273); the TK promoter of Herpes virus (McKnight (1982) Cell 31:355); the SV40 early promoter (Benoist et al. (1981) Nature (London) 290:304); the Rous sarcoma virus promoter; the cytomegalovirus promoter (Foecking et al. (1980) Gene 45:101); and the yeast gal4 gene promoter (Johnston et al. (1982) PNAS (USA) 79:6971; Silver et al. (1984) PNAS (USA) 81:5951.

Coding sequences can be operably linked to an inducible promoter. Inducible promoters are those wherein addition of an effector induces expression. Suitable effectors include proteins, metabolites, chemicals, or culture conditions capable of inducing expression.

Alternatively, a coding sequence can be operably linked to a repressible promoter. Repressible promoters are those wherein addition of an effector represses expression.

In some versions, the cell is genetically modified with a recombinant nucleic acid encoding a biosynthetic pathway gene product that is operably linked to a constitutive promoter. Suitable constitutive promoters are known in the art.

In some versions, the cell is genetically modified with an exogenous nucleic acid encoding a single protein. In other embodiments, a modified cell is one that is genetically modified with exogenous nucleic acids encoding two or more proteins. Where the cell is genetically modified to express two or more proteins, those nucleic acids can each be contained in a single or in separate expression vectors. When the nucleic acids are contained in a single expression vector, the nucleotide sequences may be operably linked to a common control element (e.g., a promoter), that is, the common control element controls expression of all of the coding sequences in the single expression vector.

When the cell is genetically modified with recombinant nucleic acids encoding two or more proteins, one of the nucleic acids can be operably linked to an inducible promoter, and one or more of the nucleic acids can be operably linked to a constitutive promoter. Alternatively, all can be operably linked to inducible promoters or all can be operably linked to constitutive promoters.

Nucleic acids encoding proteins desired to be expressed in a cell may be codon-optimized for that particular type of cell. Codon optimization can be performed for any nucleic acid by “OPTIMUMGENE”-brand gene design system by GenScript (Piscataway, N.J.).

Methods for transforming yeast cells with recombinant DNA and producing polypeptides therefrom are disclosed by Clontech Laboratories, Inc., Palo Alto, Calif., USA (in the product protocol for the “YEASTMAKER”-brand yeast transformation system kit); Reeves et al. (1992) FEMS Microbiology Letters 99:193-198; Manivasakam and Schiestl (1993) Nucleic Acids Research 21(18):4414-5; and Ganeva et al. (1994) FEMS Microbiology Letters 121:159-64. Expression and transformation vectors for transformation into many yeast strains are available. For example, expression vectors have been developed for the following yeasts: Candida albicans (Kurtz, et al. (1986) Mol. Cell. Biol. 6:142); Candida maltosa (Kunze et al. (1985) J. Basic Microbiol. 25:141); Hansenula polymorpha (Gleeson et al. (1986) J. Gen. Microbiol. 132:3459) and Roggenkamp et al. (1986) Mol. Gen. Genet. 202:302); Kluyveromyces fragilis (Das et al. (1984) J. Bacteriol. 158:1165); Kluyveromyces lactis (De Louvencourt et al. (1983) J. Bacteriol. 154:737) and Van den Berg et al. (1990) Bio/Technology 8:135); Pichia quillerimondii (Kunze et al. (1985) J. Basic Microbiol. 25:141); Pichia pastoris (Cregg et al. (1985) Mol. Cell. Biol. 5:3376; U.S. Pat. Nos. 4,837,148; and 4,929,555); Saccharomyces cerevisiae (Hinnen et al. (1978) Proc. Natl. Acad. Sci. USA 75:1929 and Ito et al. (1983) J. Bacteriol. 153:163); Schizosaccharomyces pombe (Beach et al. (1981) Nature 300:706); and Yarrowia lipolytica (Davidow et al. (1985) Curr. Genet. 10:380-471 and Gaillardin et al. (1985) Curr. Genet. 10:49). Genetic transformation systems for metabolic engineering have been developed specifically for a number of lipogenic yeasts including Mucor circinelloides (Zhang et al. 2007), Yarrowia lipolytica (Xuan et al. 1988), Rhodotorula glutinis (Li et al. 2012), Rhodosporidium toruloides (Zhu et al. 2012), Lipomyces starkeyi (Calvey et al. 2014, Oguro et al. 2015), and Trichosporon oleaginosus (Gomer et al. 2016).

Organic Substrate Conversion

An aspect of the invention includes methods of processing organics. The methods can be performed with the native, non-genetically modified yeasts or genetically modified yeasts such as those described herein. If non-genetically modified, the yeasts are preferably native lipogenic (oleaginous) yeasts, such as Lipomyces starkeyi.

The methods involve consuming certain organics while producing other organics. As used herein, “organic” refers to any organic compound, molecule, or polymer capable of being consumed or produced by a microorganism. Exemplary organics include but are not limited to carbohydrates (simple sugars, oligosaccharides, polysaccharides), nucleotides, nucleosides, nucleic acids, polypeptides, organic acids (including amino acids), and organic compounds. Specific examples of organics include glucose, glucan, xylose, xylan, arabinose, arabinan, lactic acid, glycerol, acetic acid, butanediol, ethanol, fatty acids, acylglycerols, enzymes (amylases, glucosidases, etc.), among others. As used herein, “consume” refers to the reduction of a certain component from a medium and can encompass direct uptake of the component for internal metabolic processing thereof or external processing of the component optionally followed by uptake of resulting products for internal metabolic processing.

The engineered yeasts of the invention and certain lipogenic yeasts are particularly effective at consuming certain organics that other microorganisms either cannot consume or cannot do so effectively. These organics include glycerol, cellobiose, xylose, lactic acid, trehalose, and oligosaccharides. Accordingly, an aspect of the methods of the invention includes the consumption of these and other organics from the medium. In certain versions of the invention, contacting the medium with the yeast reduces an amount of any one or more of these or other organics to less than about 80%, less than about 70%, less than about 60%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 2.5%, or less than about 1% of the initial amount.

In some aspects of the invention, the medium comprises one or more components selected from glucose, glucan, trehalose, xylose, xylan, arabinose, arabinan, lactic acid, glycerol, acetic acid, butanediol, and ethanol. The medium, for example, may comprise glucose in an amount of from about 0.01 to about 100 g/L, from about 0.1 g/L to about 10 g/L, or about 1 g/L; glucan in an amount of from about 0.1 g/L to about 1000 g/L, from about 1 g/L to about 100 g/L, or about 10 g/L; trehalose in an amount of from about 0.01 to about 100 g/L or from about 0.1 g/L to about 10 g/L; xylose in an amount of from about 0.01 g/L to about 100 g/L, from about 0.1 g/L to about 10 g/L, or about 1 g/L; xylan in an amount of from about 0.05 g/L to about 500 g/L, from 0.5 g/L to about 50 g/L, or about 5 g/L; arabinose in an amount of from about 0.005 g/L to about 50 g/L; from about 0.05 g/L to about 5 g/L, or about 0.5 g/L; arabinan in an amount of from about 0.005 g/L to about 50 g/L, from about 0.05 g/L to about 5 g/L, or about 0.5 g/L; lactic acid in an amount of from about 0.15 g/L to about 1500 g/L, about 1.5 g/L to about 150 g/L, or about 15 g/L; glycerol in an amount of from about 0.15 g/L to about 1500 g/L, from about 1.5 g/L to about 150 g/L, or about 15 g/L; acetic acid in an amount of from about 0.005 g/L to about 50 g/L; from about 0.05 g/L to about 5 g/L, or about 0.5 g/L; butanediol in an amount of from about 0.02 g/L to about 200 g/L, from about 0.2 g/L to about 20 g/L, or about 2 g/L; and/or ethanol in an amount of from about 0.005 g/L to about 50 g/L, from about 0.05 g/L to about 5 g/L, or about 0.5 g/L. Contacting the medium with a yeast may reduce an amount of any one or more of these or other organics to less than about 80%, less than about 70%, less than about 60%, less than about 50%, less than about 45%, less than about 40%, less than about 35%, less than about 30%, less than about 25%, less than about 20%, less than about 15%, less than about 10%, less than about 5%, less than about 2.5%, or less than about 1% of the initial amount.

In certain versions of the invention, the medium comprises a grain ethanol distillation stillage or a processed grain ethanol distillation stillage. The processed grain ethanol distillation stillage may be made by centrifuging distiller's wet grain therefrom, removing oil, concentrating, and filtering, or other thin-stillage processing steps described elsewhere herein or known in the art. The concentrating may comprise evaporating. In some versions, the processed grain ethanol distillation stillage comprises thin stillage. The thin stillage may be further processed by removing oil and concentrating to generate the medium.

The medium may comprise various amounts of the grain ethanol distillation stillage or processed grain ethanol distillation stillage. In some versions, the medium may comprise at least about 5%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, at least about 99%, or about 100% grain ethanol distillation stillage or processed grain ethanol distillation stillage. The grain ethanol distillation stillage or processed grain ethanol distillation stillage may be diluted with water or other solvents.

The engineered yeasts of the invention and certain lipogenic yeasts are particularly effective at producing certain organics that other microorganisms either cannot produce or cannot do so effectively. These organics include lipids (triacylglycerols, diacylglycerols, monoacylglycerols, fatty acids, etc.), enzymes (amylases, glucosidases, etc.), and other proteins. Particular enzymes include glycoside hydrolases, alpha-amylases (thermostable and secreted), dextranases (amylo-alpha-1,6-glycosidase), maltases, beta-1,4-glucosidases, endo-1,4-beta-D-glucanases (cellulases) or any other of the enzymes described elsewhere herein. Accordingly, an aspect of the methods of the invention includes the production of these and other organics.

The organic produced by the yeast may be separated or purified from any other component of the spent medium for downstream use in other applications. For example, enzymes produced by the yeast may be used in liquefaction of starch and/or saccharification of liquefaction-processed starch. Such enzymes may include any of the enzymes produced by the yeast as described above, such as carbohydrases. Lipid produced by the yeast may be used for producing biofuels therefrom or used as a replacement for palm or other oils in food applications or other applications. The yeast grown in the medium may themselves be harvested and processed to yield a source of protein as a replacement, for example, for soy protein or as a source of long-chain polyunsaturated fatty acids for fish grown in aquaculture.

The spent medium may also be mixed, either alone or with other liquids (such as thin stillage), with starch as a backset for liquefaction of the starch. The reduction in dissolved organics by virtue of the yeast consumption reduces the build-up of organics in grain ethanol production systems as a whole and in the liquefaction fermentation in particular.

EXAMPLES

Background and Overview

The existence of an annotated genome for Lipomyces starkeyi greatly facilitates cloning and homologous expression, but even with a complete or nearly-complete genome, various problems are encountered in cloning and expressing target genes.

One aspect of a suitable cloning strategy involves overexpressing endogenous genes involved in lipid production in L. starkeyi under constitutive promoters. Genomic DNA (gDNA) can be a preferable source for gene amplification, because all introns should be natively excised, and genomic DNA preparation is faster and cheaper than creating cDNA libraries. However, certain introns may have regulatory functions or their presence may impede or promote the post-transcriptional processing, subsequent protein translation, or stability of the transcript when overexpressed. Therefore, some gene targets are preferably cloned from cDNA and other targets are cloned from gDNA.

Another issue to consider in cloning involves possible alternate start codons present in the sequences of transcribed mRNA of certain gene targets. As an example, both GUT1 and DGA1 of L. starkeyi have two possible initiator methionine sites differing by a respective 15 and 156 base pairs upstream from the sequence annotated on the Joint Genome Institute site. Detailed sequence alignments with orthologs of these genes in yeast species with well-annotated sequences are inconclusive, owing to the large divergence of L. starkeyi from other yeast species and the high degree of variability at the N-terminus of these proteins. Hence, in such situations, both versions of these genes are cloned. As shown below, results sometimes demonstrate a large difference in lipid content, as in the case for the two DGA1 variants, whereas others, such as the two GUT1 variants, behave similarly.

It is not evident a priori whether genes from cDNA can be amplified under all conditions. For example, seven out of nine gene targets from cDNA could be amplified from cDNA derived from standard yeast cultures growing in liquid (yeast peptone dextrose) YPD media. However, one construct required gDNA as a cloning template. The exception was ACC1, which could not be amplified as a product from this cDNA library (as deemed by agarose gel electrophoresis) despite many PCR optimization efforts. Amplification of the gene was possible with the same primers when gDNA was used as the template. When L. starkeyi was cultivated under highly lipogenic conditions and a new cDNA library created from these cells, amplification of ACC1 was successful. Such evidence indicates that Acc1 is not constitutively expressed and that expression of ACC1 is inducible under lipogenic conditions. This finding emphasizes the importance of ACC1 as an important gene target for enhancing lipid biosynthesis.

Generation of vectors involves assembly of 4 to 6 fragments to create the desired gene cassettes using the well-established “Gibson” method for in vitro enzymatic assembly of DNA fragments (Gibson et al. 2009). Cloning attempts can be unsuccessful in producing any of the desired constructs. Gel purification methods to isolate amplified genes can introduce errors in DNA terminal regions. Therefore, gel extraction of DNA fragments and column PCR purification are preferred to improve the purity and concentration of the PCR products used in the assembly reaction.

Correct and complete constructs of the desired cassettes can be identified by colony PCR. This can be accomplished through colony PCR by amplifying either parts of the construct or the entire construct. During routine screening and sequencing, some of the construct candidates can contain partial cassettes (i.e. some will be missing part or all of one or more of the assembly components). To avoid selecting these partial constructs, it is preferable to use colony PCR for the entire cassette (instead of portions of the cassette). That way only candidates containing the appropriately sized insert are then sequenced.

L. starkeyi is cultivated under special conditions and genetic transformation is optimized in order to obtain transformants with genes integrated into the genome (Calvey et al. 2014). L. starkeyi can be transformed relatively easily with a base vector that contains only essential elements as well as a selectable marker. An exemplary base vector is represented by SEQ ID NO:91. Success depends upon having cells at an appropriate stage of development, at an appropriate cell density and with the correct ratio of cells to DNA. Transformation conditions are systematically evaluated for each method used to determine cell density, and for the activity and condition of critical reagents such as salmon sperm DNA.

In native strains of L. starkeyi, each DNA expression cassette integrates either randomly via non-homologous end joining (NHEJ) or in a targeted manner via homologous recombination to create a transformant. In native strains of L. starkeyi, NEHJ integration occurs much more frequently than homologous recombination. Even genes that normally increase lipid production when overexpressed from most integration sites can generate transformants with reduced lipid production relative to the wild-type when integrated randomly into various sites. Many strains are therefore screened under controlled conditions in order to obtain those with improved performance.

Nile Red fluorescence can be used as a rapid assay for cells or strains of cells showing greater relative lipid accumulation. However, the assay is highly variable, and it is important to conduct the trials under specific conditions. Selection of media that will enable identification of strains with the capacity for elevated lipid production on stillage is particularly critical. Some types of rich media used to cultivate L. starkeyi, such as YPD or those based on modified thin stillage (mTS), have intrinsic fluorescent properties that interfere with the proper quantification of the bona fide Nile Red fluorescent signal from the cells. Moreover, unmodified thin stillage contains significant amounts of corn oil and lipids from the hydrolysis of Saccharomyces cerevisiae. A partial solution to this problem is to perform a series of washes to remove the media from the cells, followed by suspension of the cells in H₂O. This treatment can eliminate interference due to media components that can be removed by washing. As described elsewhere herein, other methods can be used to reduce background fluorescence.

When examining cultures for increased lipid accumulation it is important to distinguish higher levels of lipid due to higher cell density from higher levels of lipid due to higher lipid content per cell. The fluorescence response is therefore normalized to the cell density.

Effects of Medium Components

The fluorescence assay is intended to identify transformants that overproduce lipid when cultivated on an industrial medium composed in part or in whole of thin stillage. Medium components can strongly affect the fluorescence assay for intracellular lipid by increasing or decreasing intracellular lipid production. When screening for a transformant with the capacity for increased lipid production, it is more difficult to identify improved mutants when the medium enables the cells to accumulate high levels of lipid than when native cells normally produce relatively little lipid under the growth conditions.

For example, wild-type, untransformed L. starkeyi cultivated in a defined minimal medium using an easily assimilated carbon source and a low amount of a poorly assimilated nitrogen source would produce a high level of lipid. The same organism cultivated with the same carbon source but an amount of readily assimilated nitrogen sufficient for cell growth would accumulate less lipid as illustrated by published studies (Calvey 2016).

It is easier to identify a transformant with increased capacity for lipid production when it is cultivated in a medium that allows lower lipid accumulation than in a medium that enables higher lipid accumulation.

As taught elsewhere in this disclosure, the relationship between the amount and the source of the carbon and the nitrogen provided to the cells can affect growth and lipid production in complex ways. Moreover, media used in certain commercial applications will include a complex mixture of glycerol, cellobiose, trehalose, xylose, xylitol, acetic acid residual corn oil and oligosaccharides derived from residual starch, hemicellulosic and cellulosic components from corn along with hydrolysis products from lysed yeast cells. In practice it is not reasonable to predict how strains or transformants will perform on a complex medium of such composition by screening their performance against simple or complex media composed of typical laboratory substrates such as glucose, yeast extract, peptone or other common medium constituents. For this reason, empirical testing is important to identify media that is representative of the industrial substrate and appropriate for strain screening. These considerations were addressed with various media as described below.

Six types of growth media were examined to determine how they influenced the native lipid accumulation of L. starkeyi over a 3-day fermentation period. The types of media included in the analysis were M1 (LN), M2 (LN), M3 (HN), M4 (HN), YPD, and mTS. M1 (LN) is a minimally defined low nitrogen media containing 1.72 g/L of yeast nitrogen base, 0.417 g/L ammonium sulfate 0.179 g/L urea, and 30 g/L of dextrose. The M1 (LN) formulation is nitrogen limiting and gives a C:N ratio of approximately 150:1. M2 (LN) is a low nitrogen media identical to YPD but containing only 3.64% of the amount of yeast extract that YPD contains and only 1.82% of the amount of peptone that YPD contains. Converted to grams/liter, M2 (LN) contains 0.364 g/L of yeast extract and 0.364 g/L of peptone. The amount of dextrose in M2 (LN) is the same as in traditional YPD (20 g/liter). The M2 (LN) formulation is nitrogen limiting and gives a C:N ratio of approximately 70:1. M3 (HN) and M4 (HN) are high nitrogen-containing versions of M1, with M4 HN containing peptone. More specifically, M3 (HN) contains 6.7 g/L yeast nitrogen base, 2.145 g/L urea, and 30 g/L dextrose. M4 HN media contains 6.7 g/L yeast nitrogen base, 2.145 g/L urea, 3.0 g/L peptone, and 30 g/L dextrose. YPD is yeast peptone dextrose media. mTS is modified thin stillage. The mTS was prepared by clarifying thin stillage to remove oil by skimming, boiling to concentrate the stillage, removing precipitates produced by the boiling, autoclaving, and removing precipitates generated during the autoclaving.

As shown in FIG. 4, the type of media greatly influences the basal lipid production of L. starkeyi NRRL Y-11557, even if nitrogen is not considered limiting. These wild-type cells appear to accumulate a moderate amount of lipids (≈30%) when cultivated in mTS during extended fermentation times, despite its nitrogen content. The mildly lipogenic property of mTS with L. starkeyi NRRL Y-11557 is likely due to the presence of glycerol and/or other compound(s).

The choice of a screening media should be done carefully. Choosing a media limiting in nitrogen could mask small lipogenic effects of certain genes, while media high in nitrogen or complexity may suppress those effects. Likewise, even media that is not nitrogen limiting can be slightly lipogenic, as seen in M3 (HN) media, because the lack of some nutrients can induce lipogenesis.

In light of these considerations, transformants of NRRL Y-11557 are screened using mTS medium to identify yeast strains that convert the soluble organics and sugars to other products. Evaluation on this medium also eliminates the possibility that some transformants perform well during screening on synthetic media but present significantly dampened or null effects when grown on a commercially relevant fermentation stream. Transformants are also screened using YPD to control for any possible variation in various sources of mTS.

Gene Cassette Selections and Primer Design

Gene cassette integration vectors are designed using a base vector as shown in FIG. 5 and having a sequence of SEQ ID NO:91. The base vector contains an origin of replication (Ori) and a kanamycin resistance cassette that permits maintenance and propagation in bacteria. In addition, it contains two multiple cloning sites (MCS) and two modified LoxP sites (RE and LE) that flank the strong constitutive LsTDH3 promoter coupled to a codon optimized nourseothricin (NAT) resistance gene and its respective transcription terminator region.

Measures are taken to ensure no antibiotic resistance gene is incorporated in the final yeast strain. The bacterial kanamycin resistance gene is not integrated into the yeast genome if it is interrupted by restriction digestion prior to transformation. The presence of the loxP sites enables excision of the NAT resistance gene after genome integration. The LoxP sites themselves are modified (i.e. dead) such that the product after one recombination event resists further recombination, thereby protecting the genomic integrity of the organism. The gene overexpression cassettes therefore include a constitutive promoter, the gene(s) of interest, and one or more transcription terminator regions inserted into one of the MCSs.

Genes are overexpressed to increase lipid production under nutrient-rich conditions. These include: acetyl-coenzyme-A carboxylase (LsACC1), delta-9 acyl-CoA desaturase (LsOLE1), ATP-citrate lyase alpha and beta subunits (LsACL1/LsACL2), two variants of glycerol kinase (LsGUT1-1602) and (LsGUT1-1617), two variants of diacylglycerol acyltransferase (LsDGA1-1233) and (LsDGA1-1389) having different start sites, and malic enzyme cloned from genomic DNA (LsgME) and cDNA (LscME), among other genes described herein. Precise promoter, gene, and terminator sequences are selected based on Illumina RNAseq data and knowledge of promoter strength and expression patterns in this organism. All contain a single promoter, gene, and terminator region, with exception to the LsAcl1/LsAcl2 construct, which involves a bidirectional promoter expressing the two genes with different transcription terminator regions. These sequences are then analyzed for the presence of specific restriction digest sites to determine into which one of two MCSs contained in the base vector they would be cloned. This step facilitates future subcloning into other vectors. For example, the diacylglycerol acyltransferase (LsDGA1) construct is capable of being inserted upstream of the loxP site using the Sbf1 restriction enzyme to linearize the vector. Other constructs are capable of being inserted downstream of the opposing loxP site, using RsrII and AvrII to linearize the vector. The desired sequence combinations and restriction enzyme sites are entered into the NEBuilder® assembly tool (nebuilder.neb.com/) with a minimum overlap setting of 20 base pairs to construct the primer sequences for performing the Gibson assembly reaction.

Schematic of the Pipeline for Creating and Characterizing Strains

An assembly line of sequential steps to create metabolically engineered yeast is shown in FIG. 6. These steps included target gene, promoter, and terminator selection, molecular biology techniques (PCR, Gibson assembly), yeast transformations, selection, cataloging and storage, Nile Red screening, and further validation assays.

gDNA Extraction and cDNA Library Creation:

A Masterpure™ Yeast DNA Purification Kit (Epicentre, Madison, Wis.) is used to extract L. starkeyi gDNA. Nitrogen rich (YPD) or nitrogen limited (YPD 70:1 (C:N)) cultures are used for RNA extraction. The YPD 70:1 media contain only 3.64% and 1.82% percent of the yeast extract and peptone as YPD, respectively. A freshly saturated 5 mL culture of L. starkeyi grown under constant agitation at 30° C. is pelleted by centrifugation, washed, suspended in 5 mL of sterile H₂O, then used to inoculate 50 mL of either YPD or YPD 70:1 media in a 125 mL shaker flask≈0.8 OD₆₀₀ and allowed to incubate overnight at 30° C. under 225 rpm. Cells are observed microscopically to determine lipid production in the YPD 70:1 media as compared to the YPD media, and the OD₆₀₀ is measured to calculate the quantity of cells to use in the RNA extraction protocol. RNA is extracted using an RNeasy Mini Kit (Qiagen), following enzymatic disruption. cDNA is synthesized from these RNA preparations using a QuantiTect® Reverse Transcription Kit (Qiagen), following the instructions of the manufacturer.

PCR of Fragments and Gibson Enzymatic Assembly:

The base vector (pXC301—FIG. 5—SEQ ID NO:91) linearized with the enzymes listed in Table 2 is used to clone L. starkeyi genes in conjunction with the “Gibson method” for in vitro enzymatic assembly of DNA fragments. All PCR amplifications are performed using Phusion High Fidelity Taq polymerase (NEB) and the manufacturer protocol in either 5× Phusion GC buffer (ACC1) or 5× Phusion buffer (all others) using the annealing temperatures in Table 2. Annealing steps are carried out using the lowest T_(m) of the primer pair, or the experimentally optimized annealing temperature, where appropriate. The reaction products are analyzed by agarose gel electrophoresis containing ethidium bromide and subsequently visualized and photographed. Successful reactions of identical fragments are pooled and then all samples (including the digested base vector) are subjected to a PCR cleanup column (Qiagen), and then quantified on a Nanodrop 2000 instrument (Thermo Scientific). The vector and inserts are then added in equimolar quantities (0.1 pmoles/fragment) in a separate tube, and the final volume adjusted to 20 μL by the addition of 15 μL premade Gibson assembly reaction mix and water. All reactions are allowed to incubate at 50° C. for one hour, and then 5 μL of the assembly reaction is used to transform 20 μL of Endura™ DUO competent cells (Lucigen) using standard techniques. Transformants are selected on LB plates containing kanamycin, and positive candidates are identified by colony PCR and sent for sequencing confirmation.

TABLE 2 Summary of Gene Targets, Promoters, and Terminators with Cloning Information Promoter and Cloning Enzymes for Target Teminator PCR Annealing Digest Yeast Gene Full Name Pairings Temperature Enzymes Transformation ACC1 Acetyl-coenzyme-A FBA1 Promoter 55-64° C. RsrII and AsiSI carboxylase ACC1 67° C. AvrII FBA1 Terminator 55-64° C. OLE1 Delta-9 acyl-CoA GLN1 Promoter 60° C. RsrII and AsiSI desaturase OLE1 63° C. AvrII GLN1 Terminator 60° C. ACL1 and ATP-citrate ENO1 Promoter 57° C. RsrII and AsiSI ACL2 lyase, alpha and ACL1 58° C. AvrII beta subunits ATPase Terminator 64° C. ACL2 58° C. TPI Terminator 65° C. Glycerol Glycerol Kinase ATPase (3900) 55.3-61.2° C. RsrII and AsiSI Kinase 1602 1602 Variant Promoter AvrII Glycerol Kinase 63.9-67° C. ATPase (3900) 62.75-66.25° C. Terminator Glycerol Diacylglycerol ATPase (3900) 58° C. RsrII and AsiSI Kinase 1617 acyltransferase Promoter AvrII 1617 Variant Glycerol Kinase 65° C. 1617 ATPase (3900) 65° C. Terminator DGA1 Diacylglycerol TEF1 Promoter 60° C. RsrII and AsiSI 1233 acyltransferase DGA1 72° C. AvrII 1233 Variant TDH3 Terminator 70° C. DGA1 Diacylglycerol TEF1 Promoter 60° C. SbfI XmaI/AvrII 1389 acyltransferase DGA1 72° C. 1389 Variant TDH3 Terminator 70° C. gMalic Malic Enzyme TDH3 Promoter 60° C. SbfI XmaI/AvrII Enzyme (gDNA) gMalic Enzyme 60° C. TDH3 Terminator 60° C. cMalic Malic Enzyme TPI (196787) 62° C. RsrII and AsiSI Enzyme (cDNA) Promoter) AvrII cMalic Enzyme 58° C. TPI (196787) 66° C. Terminator

Vectors are linearized so the entire target gene cassette, including the loxP flanked region, randomly integrates into the L. starkeyi genome as one fragment. Table 2 lists restriction enzymes for linearization. Linearized DNA is ethanol precipitated and suspended in TE to increase its concentration (>160 nM) and purity. To transform the cells, a procedure based on the lithium acetate method was used (Calvey et al. 2014, Gietz et al. 2002). A near stationary phase culture of L. starkeyi is inoculated into 50 ml YPD to between 0.6 and 0.8 OD₆₀₀ and grown overnight to reach between 3.0 and 4.0 OD₆₀₀. The culture is harvested and washed twice with 25 mL sterile water, and resuspended to 1.5 mL in sterile water or 0.1M LiAc. Aliquots of 150 μL are dispensed into 1.5 mL tubes and centrifuged. The remaining cell pellet is then suspended in 360 μL transformation mix containing 240 μL 50% w/v PEG 3350, 50 μL boiled ssDNA, 36 μL 1.0 M LiAc, and 36 μL of the desired plasmid DNA (added last). Samples are incubated at 30° C. for 3 hours, heat shocked at 40° C. for 5 minutes, and then centrifuged to remove the transformation suspension. Cells are allowed to recover in 3 mL YPD for 4 hours before being plated onto appropriate selective media. After 6 days of growth, transformants are selected, catalogued by size, and streaked onto appropriate antibiotic selection plates for creating glycerol stocks until characterization.

Yeast Lipid Screening Using Nile Red:

Both YPD and mTS are used to screen for lipid accumulation in L. starkeyi. Starter cultures are inoculated with the desired transformants in 5 mL tubes containing YPD-NAT or YPD liquid media at 30° C. under constant agitation. This lipid screening protocol is based on Nile Red fluorescence adapted from a previous study (Sitepu et al. 2012). Samples and appropriate dilutions are then prepared in a 96-well black clear-bottomed plate to contain 100 μL in each well. Nile Red is prepared as a 2 mg/mL stock solution and then diluted to a 2× working concentration (8 μg/mL). Fluorescent signals and OD₆₃₀ readings are read independently from two plate readers (BioTek™ FLx800 and BioWhittaker™ ELx808, respectively). Data is analyzed by normalizing the fluorescent signal to the OD₆₃₀ of the culture. To enable comparisons between different runs, normalized fluorescence is standardized relative to the WT culture of each group.

Lipid Extraction Analysis:

An extraction protocol is used for crude gravimetric assessments of total lipid content based on the classic Bligh and Dyer method (Bligh et al. 1959) (20). First, 2 mL of cell culture is centrifuged at 3,000 rpm for 5 minutes in 15 mL falcon tubes, and the cell pellets frozen at −20° C. until lipid extraction analysis. Thawed cell pellets are suspended in 1 mL H₂O containing 200 μL of concentrated HCl, and the suspension was heated to 90° C. for 1 hour to lyse cells. Lipids are then extracted by addition of 6 mL of a 2:1 (v:v) methanol:chloroform solution and 3 mL of 1M NaCl, followed by vortexing for 5 minutes. Tubes are then centrifuged at 3,000 rpm for 10 minutes to induce phase separation. The lipid-containing lower chloroform layer (≈2 mL) is then carefully removed using a glass Pasteur pipette, and transferred into a clean, pre-weighed, 5 mL glass vial. Finally, the extracted chloroform layer is completely evaporated by incubation in a 40° C. heat block under a constant stream of air for 1 hour. Vials are then re-weighed to determine the mass of extracted total lipids.

HPLC Analysis of Organics:

Concentrations of sugars and mTS metabolites (including glucose, xylose, cellobiose, arabinose, xylitol, ethanol, glycerol, lactic acid, and acetic acid) are determined by high performance liquid chromatography (HPLC) using an Agilent 1100 Series auto sampler, pump, and refractive index detector, with a Bio-Rad Aminex HPX-87H ion exclusion column (300×7.8 mm) held at 65° C. The mobile phase is 0.01N H₂SO₄ at a flow rate of 0.6 mL/min. Samples are diluted 1:10 prior to injection.

Selection of a Yeast Platform

The constituents of thin stillage obtained from a supplier were characterized in order to better monitor the consumption of organics during fermentation of engineered yeast strains. It was discovered that mTS contains between 18.6 to 20.5 g/L glycerol, among other components. To establish a yeast platform for bioproces sing of mTS and metabolic engineering, the growth performance of several strains of L. starkeyi on different media was monitored. All of them grew well on starch but the Y-11558 strain grew slightly faster (Table 3).

When challenged with glycerol as a carbon source, none of the South African strains (Y-27493, 27494 and 27495) grew, and Y-11558 was much slower (μ=0.047; Td=21 h). See FIG. 7. However, mutagenesis and serial subculturing reduced the doubling time of Y-11557 to 9.9 h on glycerol. These findings established that L. starkeyi grows on glycerol, a major component of mTS, and that adaptation increases growth rates. Based on these results and given that the genome of L. starkeyi NRRL Y-11557 has been sequenced (Grigoriev et al. 2012 and DOEJGI 2011), this strain was selected as the exemplary platform yeast for metabolic engineering.

TABLE 3 Doubling Times of Different Lipomyces starkeyi Strains Grown on starch Strain Doubling Time (Hrs) μ Y-1388 3.56 0.28 Y-11557 3.60 0.28 Y-11558 3.36 0.30 Y-27493 3.52 0.28 Y-27494 3.97 0.25 Y-27495 4.28 0.23 Metabolic Engineering and Screening

The next objective was to modify the physiology of L. starkeyi so that it would generate lipids under high nitrogen conditions, such as those found in thin stillage (TS) and modified thin stillage (mTS). As described in Table 2, specific genes targets were selected with constitutive promoter and terminator pairings based on knowledge of the L. starkeyi genome, its lipid biochemistry, and gene expression profile under these conditions. These were all cloned into target vectors and transformed into L. starkeyi. Since the vector integrates at random within the genome, each transformant might display different lipid biosynthetic capabilities based simply upon the site of genomic integration, or on the number of copies introduced within the genome. It was hypothesized that although gene cassettes conferring genuine lipogenic effects could occasionally integrate into unfavorable regions that could mask their effect, the average normalized fluorescence of that particular transformant pool should be somewhat higher than the average of the WT and base vector transformed strains. In addition, there may also be more variation among the transformants of these genes than those with no effect, since each transformant could have different degrees of increased lipid biosynthesis, as opposed to genes with null effects. Following this logic, a total of 234 transformants were screened from the pool of metabolically engineered strains for Nile Red fluorescence when cultivated on YPD (234), mTS (11), or both (145). The screening was performed over the course of 2 (YPD) or 3 (mTS) days. The results of this preliminary screening are shown in FIG. 8A, which displays the top 50% performers of each gene. Three gene targets (DGA1-1233, DGA1-1389, and ACC1) had either large standard deviations, higher relative normalized fluorescence (1.5-2 times higher), or both when compared to the WT yeast transformed with the base vector. This behavior was independent of the screening medium for DGA1-1233 and ACC1. Additionally, DGA1-1389, GUT1-1617 and ACL1/ACL2 displayed moderate standard deviations when screened in mTS media. The complexity of mTS likely contributed to this phenomenon. In general, however, transformants that performed well in YPD media also performed well in mTS media. Considering the variability of thin stillage across ethanol plants, this is encouraging because it implies that the engineered strains have the flexibility to overproduce lipids in various types of media. In fact, a total of 12 transformants were identified that exhibited one full standard deviation higher normalized fluorescence compared to the empty vector transformed yeast at the end of the growth phase when cultivated on both YPD and mTS. Eight of these are DGA1-1233 transformants, while the other 4 are ACC1 transformed strains.

In order to obtain a more statistically significant analysis of these results, the top performers of each gene were rescreened in triplicate in mTS. The results of this analysis are shown in FIG. 8B, and clearly demonstrate increased normalized fluorescent signals relative to the WT in DGA1-1233 6L, GUT1-1602 6L, and GUT1-1617 2L. In these transformants, it was also confirmed that the entire cassette had integrated into the genome by PCR amplification from genomic DNA using primers specific to the cassette. All had the expected fragment (data not shown).

Effects of Overexpressing Glycerol Kinase in L. Starkeyi

The presence of sugars or oligosaccharides can repress glycerol utilization in some yeasts, so overexpressing the glycerol kinase gene (GUT1) in L. starkeyi could increase glycerol utilization if that were the rate limiting step. When this hypothesis was tested, L. starkeyi transformants showed increased lipid content by Nile Red fluorescence, but presented lower growth rates. In screening about twelve GUT1-1602 and GUT1-1617 transformants for growth on thin stillage plates, one GUT1-1617 transformant, Ls-11, appeared to grow relatively faster than the others. This strain was selected to use in shake flask and 3-L bioreactor trials to compare against the WT strain. Ls-11 showed higher cell growth and glycerol utilization rates as compared to WT cells in shake flasks (FIG. 9). The cells from the 200 ml shake flasks were then used to inoculate 200 ml of medium in 3-L bioreactors. In the bioreactor studies glycerol utilization by the Ls-11 transformant was initially faster. Besides these characteristics, the Ls-11 transformant accumulated larger liposomes when examined microscopically, and formed pseudomycelia structures (FIG. 10B).

It was hypothesized that in the GUT1 transformant, glycerol kinase shunts glycerol directly towards triglyceride production via glycerol-3-phosphate, and that this accounts for higher lipid accumulation with lower growth rates. To increase the growth rate on glycerol glycerol-3-phosphate dehydrogenase (GUT2) can also be overexpressed, as described in subsequent sections. Overexpression of GUT1 alone has complex and differing effects on the growth and morphology of L. starkeyi. Different transformants of GUT1 alone show various rates of growth and increased lipid accumulation, some of which are superior to the WT or Ls-11.

Remarkably, L. starkeyi is capable of using cellobiose, trehalose, amylodextrins, cellulo-oligosaccharides, xylose, xylan oligosaccharides and glycerol—the primary carbohydrate sources present in thin stillage. The fact that L. starkeyi effectively consumes all of the oligosaccharide components and all of the glycerol in thin stillage highlights the importance and bioprocessing capabilities of this organism.

Evaluation of Other Cellular Features of DGA1-Transformed Strain

To gain further insight into the physiology of the metabolically engineered strains, a deeper evaluation into the DGA1-transformed strain (DGA1-1233 6L) was performed by evaluating its whole crude lipid content, dry cell weight, growth rate, consumption of organics, and cellular morphology relative to the WT when cultivated in mTS in a bioreactor. The DGA1-1233 6L strain grew slightly slower than the WT, leading to marginally reduced glycerol and cellobiose utilization rates (FIG. 11). Nevertheless, both strains consumed all of the available oligosaccharides and carbon sources present in mTS within five days, except for trace amounts of lactic acid (data not shown). When the cells were examined under the microscope, significantly more liposomes were observed in the DGA1-1233 transformant than the WT (FIG. 11). Remarkably, it was found that overexpression of DGA1 increased the final lipid content from 8.25 g/L to 22.7 g/L, which is an increase of about 14.5 g/L or 275%. This also correlates to an increase in the lipid content (g lipid/g dry cell weight) from approximately 30% to 85% (FIG. 12). It is hypothesized that overexpression of DGA1 is seeding liposome formation, and this in turn is increasing the lipid carrying capacity of the cells. Taken together, the present examples have demonstrated the creation of a DGA1-1233 engineered strain of L. starkeyi capable of efficiently converting mTS into cell mass with nearly 85% lipid content and 22.7 g/L lipids. This was also accomplished without optimization of culturing conditions (aeration, pH, temperature, etc.), which will surely lead to further improvements in lipid production and productivity.

Improved Screening by Substituting Bodipy Dye for Nile Red

Nile Red dye is useful in identifying engineered yeast strains that produce more lipid when cultivated on modified thin stillage (mTS), but it has several limitations: First, thin stillages from different plants vary greatly, and this variance can affect the response of the Nile Red assay. Stillages are altered by the method and extent of corn oil extraction, the extent of stillage backset, and whether clarification, and/or concentration is employed. Each of these factors affect cell growth, lipid production and the response of the Nile Red assay. Second, the mTS medium used in the screens can interfere with the Nile Red fluorescent signal, which necessitates washing cells prior to dye addition. Third, Nile Red dye itself is unstable, and signal loss occurs within several minutes following addition. Finally the number of handling steps reduces throughput in sample processing. All of these factors are exacerbated because random integration of genes into the chromosome requires examining many transformants in order to identify the top performers. An effective screening assay must be rapid, offer similar responses on many different stillages and effective in-situ without cell harvest or washing. We therefore modified our screening process to accommodate higher sample throughput by using a different fluorescent dye, Bodipy, which is superior to Nile Red in many aspects, and by standardizing the medium for screening.

Bodipy (boron-dipyrromethene) fluorescent dyes are much more sensitive and stable than Nile Red. They have been used successfully for conducting in vivo lipid trafficking and accumulation studies. One Bodipy variant (4,4-Difluoro-1,3,5,7,8-Pentamethyl-4-Bora-3a,4a-Diaza-s-Indacene) is ideal for detecting neutral lipids, such as those that accumulate in the liposomes of L. starkeyi. We established a new screening methodology in which Bodipy dye (0.6 μg/mL) is added directly to a synthetic thin stillage (sTS) to mimic cultivation in mTS under more consistent conditions. Synthetic thin stillage is composed of 6.7 g/L yeast nitrogen base with ammonium sulfate and amino acids, 20 g/L glycerol, and 6 g/L cellobiose. This method enables a 6.5 fold higher throughput in screening. It also requires fewer steps, as samples from actively growing cultures can be immediately assessed for fluorescence without washing off stillage prior to dye addition.

We also developed an improved automated method for ranking transformants based on their raw fluorescence with Bodipy. In short, samples are normalized by dilution to a target OD630 and then measured for fluorescence once a day for four days. An algorithm is then applied to rank the transformants for easy identification of prime performers. The data can be presented as bar graphs of either entire transformant pools or replicates of the same transformants. These graphs account for the dilution factor of the cells/dye, which we refer to as fluorescence in the figures for simplicity, even though it is fluorescence following correction for dilution. This approach streamlines the data analysis process with minimal manipulation. As proof of principle, many of the same transformants that had been selected manually in Nile Red assays were also identified by this approach, along with other high performing strains that might have been overlooked based on the previous method.

Investigating DGA1 Cassette Variants on Lipid Accumulation

One of the most lipogenic cassettes discussed above overexpresses diacylglycerol acyltransferase (DGA1-1233), which was cloned from cDNA (cDGA1-1233). It employs a NAT marker for resistance to the antibiotic nourseothricin to enable selection of transformed strains. In order to facilitate overexpression of cDGA1-1233-NAT in combination with other genes—either by sequential transformations or by mating—we constructed a second DGA1-1233 overexpression cassette using an alternate resistance marker. We then determined the conditions under which L. starkeyi transformants could be recovered on plates containing an antibiotic other than nourseothricin.

We next questioned whether overexpression of cDNA or genomic DNA (gDNA) of DGA1 (gDGA1-1233) resulted in better transformants. The principal difference between the gDNA and cDNA clones of DGA1-1233 is the presence or absence of introns. Introns are known to enable alternative splicing of mRNA so a single gene can create multiple proteins, and while introns do not encode protein products, they can be integral to the regulation of gene expression.

Little is known about how or whether introns regulate gene expression in L. starkeyi. To address this, we created sibling cDGA1-1233 and gDGA1-1233 cassettes cloned from cDNA and gDNA into a vector that confers resistance to Hygromycin B. These were then transformed into L. starkeyi and the Bodipy fluorescence of the resulting transformant pools were monitored in sTS over the course of four days. Although both versions yielded more fluorescence over the wild-type strain, the gDNA version did not induce as many liposomes as the cDNA version, which indicated that the presence of introns modulated cDGA1-1233 expression. Subsequent screening tests revealed that the top cDNA transformant (cDGA1-1233 154L) outperformed the top gDNA transformant (gDGA 163M). Moreover, cDGA 154L behaved similarly to strain 6L, the top performer from the Nile Red screen. See FIG. 13. Therefore, we selected cDGA1-1233 154L as our platform strain for further development.

Deregulated Acc1 Mutants

ACC1 expression is induced under lipogenic conditions in L. starkeyi, and when overexpressed, we identified four transformants that exhibited one full standard deviation higher normalized fluorescence when compared to yeast transformed with the empty vector. However, these transformants were clearly less prodigious at producing lipids compared to our DGA1 transformants. This was surprising, since ACC catalyzes the carboxylation of acetyl-CoA into malonyl-CoA, which is a regulated commitment step in fatty acid biosynthesis.

Enzyme activity can be regulated by more factors than gene expression alone. In fact, ACC activity in S. cerevisiae and other organisms is regulated by an AMP-activated protein kinase (Snf1), which phosphorylates certain serine residues. Mutation of these residues can prevent inhibition of ACC, and increase lipid yields.

To determine if ACC could also be deregulated in L. starkeyi, we identified two possible serine phosphorylation sites in the L. starkeyi ACC1 ortholog based on the AMPK phosphorylation target motif, and created three mutated versions of the ACC1 gene (S639A, S1146A, and the double mutant S639A/S1146A). These were made because it was unknown which mutations and in what combination could deregulate Acct activity. Following transformation and fluorescence screening in yeast, we discovered that constitutive expression of the single S1146A mutant (but not S639A nor the double mutant cassette), increased average fluorescence levels, as shown in FIG. 14.

Overexpression of Acyltransferases

Given the dramatic improvement in lipid accumulation that occurs in DGA1-1233 engineered strains, we hypothesized that expression of additional genes involved in the biosynthesis of triacylglycerols might coax cellular metabolism towards additional lipid production. The DGA1 gene product carries out the third and final acylation step in triacylglycerol synthesis, so we focused our attention on the two acyltransferases that catalyze the previous reactions, namely SCT1 and SLC1. The former (SCT1) is a glycerol-3-phosphate acyltransferase that carries out the first acylation step, whereas the latter (SLC1) is a lysophosphatidate acyltransferase, which catalyzes the second acylation step. To test these genes, we constructed SCT1 and SLC1 overexpression cassettes from gDNA under the control of the CIT1 promoter/terminator pair (SCT1) or the FBA1 promoter/terminator pair (SLC1), and generated over 200 transformants from each cassette to assay for increased lipid production. These strains were evaluated on sTS medium using our Bodipy screening methodology.

Data gathered from an exemplary screen of SCT1 transformants is shown in FIG. 15. Overexpression of SCT1 caused a moderate increase in lipid accumulation under these conditions. SCT1 transformants, on average, yielded 5-10% increased lipid content as measured by Bodipy fluorescence. However, some of the top performing SCT1 strains produced fluorescent readings approximately 30% higher than the wildtype across all time points tested. Taken together, these results demonstrate that SCT1 plays a critical role in initiating triacylglycerol biosynthesis in L. starkeyi. Additionally, SCT1 is an attractive target because it utilizes glycerol-3-phosphate as a substrate, and could potentially improve the rate of glycerol utilization in feedstocks with high glycerol content, such as thin stillage. SCT1 was also introduced into other genetic backgrounds by both mating and secondary transformations, as described below, to generate strains with further improvements.

In contrast to SCT1, overexpression of SLC1 did not result in any statistically significant improvements in lipid accumulation. On average the SLC1 strains performed no better, or perhaps slightly worse, than the wild-type in terms of Bodipy fluorescence readings (FIG. 16). Growth rates of all strains were approximately similar. However, there were a few strains that performed better than any wild-type replicates (e.g. SLC1-30L, FIG. 16), which could occur if multicopy integration or specific integration sites are required for SLC1 to have a measurable impact on lipid production.

Given that overexpression of SLC1 alone does not typically increase lipid production, this suggests that the second acylation reaction catalyzed by SLC1 is not a rate-limiting or highly regulated step during the accumulation of lipids in Lipomyces. Since we have demonstrated that overexpression of SCT1 (1st acylation) and DGA1/2 (3rd acylation) have such significant effects on improving lipid accumulation, it follows that these are the more significant bottlenecks than the SLC1 reaction.

However, it remains to be seen if combinatorial expression of SLC1 with other genes may synergistically increase lipid production. It is possible that overexpression of SLC1 in a SCT1 engineered strain could further improve lipid production if the bottleneck resolved by acceleration of the first acylation step (SCT1) subsequently leads to the creation of a new rate-limiting step at the second acylation (SLC1). Alternatively, overexpression of SLC1 in a DGA1 engineered strain could also improve lipid production by introducing a metabolic “pull” towards triacylglycerol production.

Combinatorial Expression of Lipogenic Cassettes

In order to evaluate the effects of overexpressing more than one lipogenic cassette in the same organism, we pursued two strategies. First, top strains with different resistance markers were mated together and subjected to sporulation, and progeny harboring both integrated cassettes were selected on double antibiotic plates. Alternatively, top strains were also used as a platform for a second round of transformations with another cassette, as long as the resistance markers were different. The resulting double transformed strains were then evaluated in our Bodipy screen against the progenitor transformant strain for enhanced lipid production. In this way, we screened over 70 mated strains of top performers and 200 double transformed strains.

We first evaluated mated transformants overexpressing DGA1-1233 and ACC1, ACC1(S639A), and ACC1(S1146A). In some cases, the mated strains performed better than the parental strains. The biggest improvement was seen in the DGA1-1233/ACC1(S1146A) cross (FIG. 17). The DGA1-1233/ACC1(S639A) cross performed no better than the DGA1-1233/ACC1 cross and also no better than the parental DGA1-1233 strain, again suggesting that S639 plays no role in regulating ACC1. Hence, the combination of overexpressing DGA1-1233 and ACC1 in L. starkeyi enhances lipid production compared to independent overexpression of these proteins, but is particularly pronounced when ACC1 is mutated at the S1146 phosphorylation site.

We also evaluated mated transformants constitutively expressing DGA1-1233 and SCT1, and a strain with two DGA1-1233 overexpression cassettes. In both cases, each strain performed better than the parental strains. These are shown in FIG. 18, along with the wild-type and our previously identified top performer (cDGA NAT) for comparison purposes.

Combinatorial Expression of Lipogenic and Auxiliary Cassettes

We previously determined that certain cassettes resulted in no significant increase in lipid accumulation relative to control strains as deemed by Nile Red analysis in Lipomyces starkeyi. See FIG. 8. These included the dual overexpression of ATP citrate lyase subunits 1 and 2 (Acl1/Acl2), and the cDNA and gDNA versions of the malic enzyme (gME and cME). We re-evaluated these transformants in our sTS screening methodology using Bodipy and obtained similar results. We hypothesized that overexpressing these genes has little effect on lipid accumulation since they are not directly involved in the regulatory mechanisms that govern lipogenesis. However, their activities may synergistically enhance lipid accumulation in strains that have been deregulated from one or more of these mechanisms.

To test this hypothesis, we selected our top DGA1 transformant (cDGA1) to cross with select transformants overexpressing the cDNA version of the ATP citrate lyase cassette (cAcl1/2), or the cDNA and gDNA versions of the malic enzyme cassettes (cMalic Enzyme, gMalic Enzyme). After mating, the progeny and parental strains were evaluated in sTS containing Bodipy for lipid accumulation. As observed previously, the Acl1/Acl2 and malic enzyme sole transformants performed marginally better than the wild-type strain due to the presence of resistance marker integration and overexpression (FIG. 19). Sole overexpression of a resistance marker cassette can be marginally lipogenic due to a number of possibilities, including slower transformant growth and the position in which the cassette integrated in the genome. However, when coupled with overexpression of DGA1, the crossed strains performed significantly better than either of the parental strains, particularly on the third and fourth days of culture growth (FIG. 19). As a control, we also evaluated the parental DGA1 strain transformed with the empty base vector overexpressing the same resistance marker as the lipogenic transformants. The overall performance of these control strains was slightly worse than the parental DGA1 strain (FIG. 20), implying that the lipid accumulation observed in the mated strains could be synergistic, as the total improvement is the same if not higher than the individual improvements combined.

Enhanced glycerol utilization is another feature that is particularly important, due to the large amount of glycerol present in thin stillage. Glycerol Kinase (GUT1) catalyzes the phosphorylation of glycerol to glycerol-3-phosphate, and is the first step in glycerol utilization. However, when GUT1 was overexpressed in L. starkeyi, the cells presented with significantly lower growth rates, presumably due to the introduction of a metabolic bottleneck. To overcome this, we transformed a strain overexpressing GUT1 with an FAD dependent glycerol-3-phosphate dehydrogenase (GUT2), which catalyzes the second reaction in glycerol utilization by conversion of glycerol-6-phosphate to dihydroxyacetone phosphate (DHAP), and screened the resulting double transformants for growth on glycerol and lipid accumulation. Dual overexpression of GUT1 and GUT2 rescued the growth rates in approximately half of the transformants evaluated (FIG. 21), with some exhibiting superior lipid accumulation relative to the parental strains (FIG. 22). Importantly, overexpression of GUT2 alone did not significantly affect lipid accumulation (FIG. 22). One of the highly lipogenic strains (GUT1/GUT2 1L) was chosen for scale-up in shake flask experiments to better evaluate its glycerol utilization rate in media containing both glucose and glycerol as a carbon source (FIGS. 23A-23D). The results of this experiment demonstrate that the GUT1/GUT2 double transformant consumed glycerol at a faster rate than the wild-type, once glucose catabolite repression was alleviated.

The highly lipogenic nature of some of the double GUT1/GUT2 transformants was not anticipated, since enhanced glycerol utilization might diminish glycerol pools needed for triacylglyceride synthesis. One explanation for this is that only one molecule of glycerol is needed for every triacylglceride formed, and even though the wild-type strain uses glycerol as a substrate, expression of the assimilation pathway is not optimal. Biosynthesis of acyl carbon chains could be enhanced by increased metabolic carbon flux due to faster glycerol catabolism.

Overexpression of Glycerol-3-Phosphate Dehydrogenase (GPD1)

Intracellular production of glycerol involves the reduction of dihydroxyacetone phosphate (DHAP) into glycerol-3-phosphate by the NADH dependent enzyme glycerol-3-phosphate dehydrogenase (GPD1). Overexpression of GPD1 could alleviate a potential bottleneck in glycerol formation and introduce a metabolic “push” towards triacylglycerol production. Hence, we constructed a GPD1 overexpression cassette driven by a pyruvate kinase (PYK1) promoter and the cognate PYK1 terminator. This was transformed into L. starkeyi and several hundred transformants were obtained, of which a subset were selected for Bodipy analysis in sTS. The results of this are shown in FIG. 24. The transformant pool evaluated had moderately higher fluorescence over the wild-type, which became progressively more pronounced throughout the duration of the screen. In fact, by the last day the average fluorescence of the transformant pool was almost 13% higher than the wild-type. This is counterintuitive, since by this time the cells have consumed all of the cellobiose and most of the glycerol present in sTS. Lipogenic effects should be observed when the cells are consuming cellobiose and producing DHAP to convert into glycerol, not consuming glycerol. This could be explained if GPD1 favors conversion of glycerol-3-phosphate into DHAP during glycerol consumption. The DHAP could then enter the glycolytic pathway and be used to produce energy, which indirectly effects lipid levels and/or cell robustness. A similar Bodipy screen performed on media lacking glycerol but containing glucose could provide more insight into this phenomenon.

Engineering the Pentose Phosphate Pathway

To test our prediction that overexpression of 6-phospholuconate dehydrogenase (GND1) and/or glucose-6-phosphate dehydrogenase (ZWF1) could improve lipid production via increasing the cytoplasmic pool of NADPH, we constructed a plasmid to simultaneously express both genes. The plasmid was transformed into Lipomyces, and several hundred transformants were obtained. Of these, 60 colonies were selected for further screening using our sTS and Bodipy methodology. The results of this screen are shown in FIG. 25.

We found that dual overexpression of GND1 and ZWF1 leads to moderately improved lipid accumulation in Lipomyces (FIG. 25). The average fluorescence readings of all transformants outperformed the wild-type by about 10-15% at each time point. Two exceptional strains, “GND1+ZWF1 37L” and “GND1+ZWF1 26L” had fluorescent values approximately 30% and 60% higher than the wild-type, respectively. These results suggest that when engineered cells are grown on sTS, overexpression of GND1 and ZWF1 helps to “pull” glucose (derived from cellobiose or amylodextrins) towards the pentose phosphate pathway. Catabolism of glucose via this pathway generates more NADPH than via glycolysis, which increases the availability of reducing power required for lipid biosynthesis.

Generation and Use of an NHEJ-Deficient (lig4Δ) Strain for Further Metabolic Engineering

In Lipomyces starkeyi, genetic transformation occurs primarily via random integration into the genome, likely by a non-homologous end joining (NHEJ) mechanism. Previous attempts to disrupt genes of interest using homologous recombination with knockout constructs were unsuccessful. However, it is well known that disruption of the NHEJ pathway in a wide range of yeast species greatly increases homologous recombination efficiencies, and facilitates targeted deletion or insertion of genes. Knockouts of Ku70, Ku80, and/or Lig4 have all been commonly used to ablate NHEJ. Therefore, we sought to disrupt the DNA ligase LIG4 (PID_2300, SEQ ID NO:73 (nucleotide) and SEQ ID NO:74 (protein)), to generate an NHEJ-deficient strain of Lipomyces. A strain with improved homologous recombination could be used to knock out members of the beta-oxidation pathway, for example, to eliminate the ability of Lipomyces starkeyi to consume accumulated lipids.

A LIG4 knockout construct was compiled, using a LoxP-flanked NAT resistance construct bordered by 3 kb of cloned genomic DNA homologous to the upstream (promoter) and downstream (terminator) regions neighboring the LIG4 gene. The transformation rate was very low when introduced into Lipomyces, due to the large size of the construct (≈8.4 kb). A total of 22 colonies were selected for further examination to determine if they were truly LIG4 knockouts (lig4Δ). Following genomic DNA extraction and PCR genotyping, we found that only 1/22 transformants (4.5%) harbored a band consistent with replacement of the LIG4 gene by the NAT resistance construct (lig4::NAT). Thus, random integration elsewhere into the genome was the dominant mode of genetic transformation and that homologous recombination occurs only about 5% of the time even when very long flanking regions are used. Subsequent amplification and sequencing of the LIG4 locus in the putative knockout strain confirmed that gene replacement by homologous recombination occurred exactly as intended.

To determine the utility of this strain as a genetic tool, we designed two additional knockout constructs, targeting the acyl-CoA oxidase PDX1 and multifunctional enzyme (3-hydroxyacyl-CoA dehydrogenase & enoyl-CoA hydratase) FOX1 in the lig4Δ strain. These constructs utilized a LoxP-flanked HPH resistance marker, bordered by only 1 kb of cloned genomic DNA homologous to the upstream/downstream regions neighboring each respective gene. Transformation of the lig4Δ strain with these constructs resulted in about 70 colonies each. From these, a total of 18 strains were selected for analysis by PCR genotyping. Of the PDX1 transformants, we found that 7 out of 9 (78%) were confirmed as true knockouts. As for the FOX1 transformants, only 2 out of 9 (22%) were confirmed to be true knockouts. Regardless, these significantly improved homology recombination rates demonstrate that gene deletions are much easier to achieve in the lig4Δ::NAT background, and can be accomplished with shorter regions of homology.

Disruption of the β-Oxidation Pathway in L. Starkeyi

As described above, we generated a NHEJ-deficient Lipomyces strain by gene replacement of the DNA ligase LIG4 with a NAT resistance construct (lig4Δ::NAT). Using this strain as a platform, two additional transformations were carried out in order to subsequently knock out either the acyl-CoA oxidase PDX1 or the multifunctional enzyme FOX1 by homologous recombination mediated gene replacement with a LoxP-flanked HPH construct. The resulting strains were knockouts for both LIG4 and either PDX1 or FOX1 (ligΔ::NAT, pox1Δ::HPH), (lig4Δ::NAT, fox1Δ::HPH).

To test our prediction that disruption of the β-oxidation pathway could improve lipid accumulation, we subjected several replicates of validated pox1Δ or fox1Δ knockouts to our standard Bodipy screening methodology in sTS medium (FIG. 26). We found that deletion of either PDX1 or FOX1 mildly enhances lipid accumulation when cells are incubated under aerobic conditions. Average fluorescent readings of these knockout strains ranged from about 5-15% higher values that the wildtype controls. These results suggest that, in addition to overexpressing lipogenic genes, eliminating lipid consumption by the β-oxidation pathway is another viable route for improving lipid accumulation in Lipomyces starkeyi.

Overexpression of DGA2—a Second Diacylglycerol Acyltransferase

Overexpression of diacylglycerol acyltransferases, alone or in combination with other lipogenic genes, is predicted to increase lipid accumulation. Unlike Saccharomyces cerevisiae, some oleaginous yeast species (e.g. Yarrowia lipolytica) possess two or more protein encoding genes with diacylglycerol acyltransferase activity. Upon searching the genome for additional putative DGA genes, we discovered that Lipomyces starkeyi contains a second, previously unknown, diacylglycerol acyltransferase gene (DGA2, PID_6231, SEQ ID NOS: 57 and 58). The sequences of DGA1 and DGA2 are quite divergent, as DGA2 is a member of the MBOAT family (Membrane Bound O-Acyl Transferase), and possesses several transmembrane domains. DGA1 is most likely localized to liposomes, while we predict DGA2 resides in the endoplasmic reticulum.

It is unknown whether DGA1 and DGA2 might have differing metabolic roles, activities, or regulation. We therefore tested whether overexpression of the DGA2 gene was capable of increasing lipid production. A plasmid was designed to overexpress DGA2 under the control of the native Lipomyces TPI1 promoter and PGK1 terminator. Hundreds of transformants were obtained and subjected to the Bodipy screening methodology described previously. In an exemplary screen, 87 individual DGA2 transformant strains were grown and assessed for lipid accumulation as compared to wild-type replicates. We found that overexpression of DGA2 leads to significantly improved lipid accumulation in Lipomyces (FIG. 27). The average of all DGA2 transformants, which includes poor performers, still outperformed the wild-type by 5-10% on each time point. Some of the most promising strains, such as “DGA2-20L” and “DGA2-70L,” had fluorescent values 20-30% higher than the wildtype (FIG. 27). Therefore, we have identified a second diacylglycerol acyltransferase as an engineering target for increasing lipid accumulation in Lipomyces starkeyi.

Presence of Trehalose in Thin Stillage and its Utilization in Lipomyces Starkeyi

Thin stillage is a complex mixture containing a variety of short-chain oligosaccharides that are difficult to distinguish from each other using typical analytical methods (e.g. HPLC). For example, disaccharides of glucose include cellobiose, maltose, and trehalose, which differ only in the location of their glycosidic bonds. For simplicity, our synthetic thin stillage medium (sTS) includes cellobiose as the sole analog for all disaccharides which might be present. However, trehalose accumulates in Saccharomyces cerevisiae in response to many environmental stress conditions, particularly as an adaptation mechanism to ethanol tolerance. Consequently, in the yeast ethanol industry, trehalose is found among the residual sugars at the termination of fermentation. Trehalose makes up a significant portion of the remaining disaccharide fraction, referred to as the “DP2 peak” in reference to the degree of polymerization of the oligosaccharides eluted together during HPLC analysis.

Therefore, complete conversion of the organics present in thin stillage requires either addition of a trehalase enzyme or use of organisms capable of naturally utilizing trehalose as a carbon source. We have observed nearly complete disappearance of the “DP2 peak” when Lipomyces is cultured on thin stillage, which suggests that this species natively possesses the ability to consume the residual trehalose. We discovered two trehalases in L. starkeyi, which are categorized based on their predicted pH optimum: the “neutral” trehalase NTH1 (PID_4858, SEQ ID NOS: 59 and 60), and the “acidic” trehalase ATH1 (PID_4583, SEQ ID NOS: 61 and 62). Interestingly, the L. starkeyi ATH1 has a strong secretion signal, which indicates its usefulness in engineering strains for hyper-secretion of trehalase, or other glycoside hydrolases. If spent Lipomyces broth were recycled back into primary fermentation vessels, secreted trehalases would reduce the residual sugars present in the DP2 peak, resulting in increased ethanol yields and plant profitability.

Targeting Glycerol Transporters in Lipomyces Starkeyi for Enhanced Glycerol Utilization

There are multiple potential routes for glycerol assimilation in yeast. The phosphorylative pathway, which involves the glycerol kinase GUT1 and the mitochondrial FAD-dependent glycerol 3-phosphate dehydrogenase GUT2, ultimately generates DHAP for glycolysis. Simultaneous overexpression of GUT1 and GUT2 improves the rate of glycerol utilization, as described elsewhere. Another strategy for improving glycerol utilization is the overexpression of transporters involved in the uptake of glycerol into the cell. Several glycerol transporters have been identified in yeast.

The primary route for glycerol uptake in Saccharomyces is through active transport via STL1, a glycerol/H+ symporter. STL1 is a member of the major facilitator superfamily, a broad group of transporters for many substrates, which can make identification of specific genes difficult. We have identified two a glycerol/H+ symporters in Lipomyces starkeyi, referred to as STL1 (PID_114515, SEQ ID NOS:63 and 64 and STL2 (PID_201837, SEQ ID NOS:65 and 66).

A secondary route for glycerol uptake in Saccharomyces is through passive transport by FPS1, a glycerol facilitator, which is mainly used for controlled export of glycerol during osmoregulation. However, FPS1 homologs in other species with superior glycerol utilization rates (such as Pachysolen tannophilus) have been shown to be the main route of glycerol import. We have identified a FPS1 homolog in L. starkeyi (PID_67294, SEQ ID NOS:67 and 68). Interestingly, the L. starkeyi FPS1 is more similar to the Pachysolen FPS1 than the Saccharomyces FPS1, so it may function as a passive glycerol transporter by facilitated diffusion.

We have observed that when Lipomyces is grown in the presence of both glucose and glycerol, glucose is preferentially utilized first due to the effects of carbon catabolite repression. One of the methods for controlling this response arises from transcriptional regulation of glycerol transporters, which are not highly expressed while glucose is present. Transporters unconstrained by transcriptional regulation could help to improve glycerol uptake and enable simultaneous utilization of glucose and glycerol. Therefore, the STL1, STL2, and FPS1 can be overexpressed with constitutive promoters to overcome carbon catabolite repression and improve glycerol utilization rates in L. starkeyi.

Engineering Constitutive Glucoamylase Secretion

Alpha-amylase and glucoamylases are major expenses in ethanol plants, required for the hydrolysis of starch polysaccharides into fermentable glucose monomers. Interestingly, L. starkeyi is known to synthesize both dextranases and amylases. We found evidence of inducible extracellular glucoamylase activity in the supernatant of cells cultured in media containing starch, but not dextrose. This activity was also eliminated by boiling, indicating that it is the result of one or more secreted enzymes, induced by the presence of complex carbohydrates (FIG. 28 (A)). If one or more of these secreted enzymes could be engineered for high levels of secretion in L. starkeyi, then it could serve as a valuable co-product during the production of lipid. To demonstrate the feasibility of this strategy, we identified a secreted α-amylase in L. starkeyi and engineered it for constitutive expression. The supernatant of the resulting transformants exhibited glucoamylase activity independent of the culture medium, and this activity was retained following incubation for 1 hour at 70° C. (FIG. 28, (B)). Thus, we have achieved constitutive secretion of a relatively thermostable α-amylase in L. starkeyi. Optimally, this will result in a spent culture broth rich in a collection of starch degrading enzymes with exceptional processivity and substrate diversity that could be used in ethanol plants to reduce operating costs, or other related industries.

Consolidation of Transformed Traits

Combinations of gene cassettes from the top lipid producing strains described above further enhance lipid accumulation, and can be done through yeast mating. Mating techniques for Lipomyces starkeyi and isolation of spores for screening progeny enables identification of crossed strains with more than one cassette integrated in the genome without needing to create cassettes with alternate resistance markers and repeat the screening process. Nonetheless, integration vectors that confer resistance to G418 and Hygromycin B that are functional in L. starkeyi can be used. Lastly, a Lipomyces starkeyi strain that constitutively secretes a native α-amylase and could be mated to the DGA1-1233 transformant to obtain a strain that converts mTS to lipids and α-amylase. Lipids and α-amylase are products of much higher value than the mTS substrate, which currently presents a disposal cost.

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Exemplary Embodiments of the Invention

Exemplary embodiments of the invention are as follows:

Embodiment 1

A recombinant yeast comprising one or more recombinant nucleic acids configured to express one or more proteins selected from the group consisting of an acetyl-CoA carboxylase, an alpha-amylase, an ATP citrate lyase, a diacylglycerol acyltransferase, a fatty acid synthase, a glycerol kinase, a 6-phosphogluconate dehydrogenase, a glycerol-3-phosphate dehydrogenase, a malic enzyme, a fatty acyl-CoA reductase, a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate acyltransferase, a lysophosphatidate acyltransferase, a glucose-6-phosphate dehydrogenase, a beta-glucosidase, a hexose transporter, a glycerol transporter, a glycoside hydrolase enzyme, and an auxiliary activity family 9 enzyme.

Embodiment 2

The recombinant yeast of embodiment 1, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express the one or more proteins.

Embodiment 3

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol kinase and a glycerol-3-phosphate dehydrogenase.

Embodiment 4

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a diacylglycerol acyltransferase and at least one of an ATP citrate lyase and a malic enzyme.

Embodiment 5

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express an acetyl-CoA carboxylase comprising a sequence at least about 90% identical to SEQ ID NO:2.

Embodiment 6

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express an acetyl-CoA carboxylase comprising a sequence at least about 90% identical to SEQ ID NO:2, wherein the sequence comprises a residue other than serine and threonine at a position corresponding to position 1146 of SEQ ID NO:2.

Embodiment 7

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express an acetyl-CoA carboxylase comprising a sequence at least about 90% identical to SEQ ID NO:2, wherein the sequence comprises and a serine or threonine at a position corresponding to position 639 of SEQ ID NO:2 a residue other than serine and threonine at a position corresponding to position 1146 of SEQ ID NO:2.

Embodiment 8

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express one or more alpha-amylases comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:4, a sequence at least about 90% identical to SEQ ID NO:6, and a sequence at least about 90% identical to SEQ ID NO:8.

Embodiment 9

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express an ATP citrate lyase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:10 and a sequence at least about 90% identical to SEQ ID NO:12.

Embodiment 10

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a diacylglycerol acyltransferase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:14, a sequence at least about 90% identical to SEQ ID NO:16, and a sequence at least about 90% identical to SEQ ID NO:58.

Embodiment 11

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a diacylglycerol acyltransferase comprising a sequence at least about 90% identical to SEQ ID NO:14 and devoid of a sequence corresponding to positions 1-52 of SEQ ID NO:16.

Embodiment 12

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a fatty acid synthase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:18, a sequence at least about 90% identical to SEQ ID NO:20, a sequence at least about 90% identical to SEQ ID NO:22, and a sequence at least about 90% identical to SEQ ID NO:24.

Embodiment 13

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol kinase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:26 and a sequence at least about 90% identical to SEQ ID NO:28.

Embodiment 14

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol kinase comprising a sequence at least about 90% identical to SEQ ID NO:26 and devoid of a sequence corresponding to positions 1-5 of SEQ ID NO:28.

Embodiment 15

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a 6-phosphogluconate dehydrogenase comprising a sequence at least about 90% identical to SEQ ID NO:30.

Embodiment 16

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol-3-phosphate dehydrogenase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:32 and a sequence at least about 90% identical to SEQ ID NO:56.

Embodiment 17

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol kinase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:26 and a sequence at least about 90% identical to SEQ ID NO:28 and a glycerol-3-phosphate dehydrogenase comprising a sequence at least about 90% identical to SEQ ID NO:56.

Embodiment 18

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a malic enzyme comprising a sequence at least about 90% identical to SEQ ID NO:34.

Embodiment 19

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a diacylglycerol acyltransferase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:14, a sequence at least about 90% identical to SEQ ID NO:16, and a sequence at least about 90% identical to SEQ ID NO:58, in combination with at least one of an ATP citrate lyase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:10 and a sequence at least about 90% identical to SEQ ID NO:12 and a malic enzyme comprising a sequence at least about 90% identical to SEQ ID NO:34.

Embodiment 20

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a fatty acyl-CoA reductase comprising a sequence at least about 90% identical to SEQ ID NO:36.

Embodiment 21

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a delta-9 acyl-CoA desaturase comprising a sequence at least about 90% identical to SEQ ID NO:38.

Embodiment 22

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol-3-phosphate acyltransferase comprising a sequence at least about 90% identical to SEQ ID NO:40.

Embodiment 23

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a lysophosphatidate acyltransferase comprising a sequence at least about 90% identical to SEQ ID NO:42.

Embodiment 24

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glucose-6-phosphate dehydrogenase comprising a sequence at least about 90% identical to SEQ ID NO:44.

Embodiment 25

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a beta-glucosidase comprising a sequence at least about 90% identical to SEQ ID NO:46.

Embodiment 26

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a hexose transporter comprising a sequence at least about 90% identical to SEQ ID NO:48.

Embodiment 27

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a glycerol transporter comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:66, a sequence at least about 90% identical to SEQ ID NO:66, and a sequence at least about 90% identical to SEQ ID NO:68.

Embodiment 28

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express one or more glycoside hydrolase family 5 enzymes comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:50 and a sequence at least about 90% identical to SEQ ID NO:52.

Embodiment 29

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express a trehalase comprising a sequence selected from the group consisting of a sequence at least about 90% identical to SEQ ID NO:60 and a sequence at least about 90% identical to SEQ ID NO:62.

Embodiment 30

The recombinant yeast of any prior embodiment, wherein the one or more recombinant nucleic acids comprises one or more recombinant genes configured to express an auxiliary activity family 9 enzyme comprising a sequence at least about 90% identical to SEQ ID NO:54.

Embodiment 31

The recombinant yeast of any prior embodiment, wherein at least one of the one or more recombinant nucleic acids comprises a recombinant gene comprising a constitutive promoter or an inducible promoter.

Embodiment 32

The recombinant yeast of any prior embodiment, wherein at least one of the one or more recombinant nucleic acids comprise a recombinant gene comprising a promoter operably linked to a coding sequence of at least one of the one or more enzymes, wherein the promoter has a sequence selected from the group consisting of a sequence at least about 90% identical to any one of SEQ ID NOS:75-84.

Embodiment 33

The recombinant yeast of any prior embodiment, wherein at least one of the one or more recombinant nucleic acids comprise a recombinant gene comprising a terminator operably linked to a coding sequence of at least one of the one or more enzymes, wherein the terminator has a sequence selected from the group consisting of a sequence at least about 90% identical to any one of SEQ ID NOS:85-90.

Embodiment 34

The recombinant yeast of any prior embodiment, wherein the yeast exhibits increased expression of at least one of the one or more enzymes relative to a non-recombinant control.

Embodiment 35

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of one or more native enzymes in the yeast selected from the group consisting of a delta-9 acyl-CoA desaturase, a glycerol-3-phosphate dehydrogenase, an acyl-CoA oxidase, a 3-hydroxyacyl-CoA dehydrogenase, and an enoyl-CoA hydratase.

Embodiment 36

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of a native delta-9 acyl-CoA desaturase comprising a sequence at least about 90% identical to SEQ ID NO:38.

Embodiment 37

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of a native glycerol-3-phosphate dehydrogenase comprising a sequence at least about 90% identical to SEQ ID NO:56.

Embodiment 38

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of a native acyl-CoA oxidase comprising a sequence at least about 90% identical to SEQ ID NO:70.

Embodiment 39

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of a native 3-hydroxyacyl-CoA dehydrogenase comprising a sequence at least about 90% identical to SEQ ID NO:72.

Embodiment 40

The recombinant yeast of any prior embodiment, wherein the yeast comprises a modification that reduces or ablates the activity of a native enoyl-CoA hydratase comprising a sequence at least about 90% identical to SEQ ID NO:72.

Embodiment 41

The recombinant yeast of any prior embodiment, wherein the yeast exhibits a property selected from the group consisting of increased lipid production, increased lipid secretion, increased carbohydrase production, increased carbohydrase secretion, increased growth rate, increased glycerol consumption, increase trehalose consumption, and increased cellobiose consumption relative to a non-recombinant control.

Embodiment 42

The recombinant yeast of any prior embodiment, wherein the yeast is a recombinant lipogenic yeast.

Embodiment 43

The recombinant yeast of any prior embodiment, wherein the yeast is a recombinant Lipomyces starkeyi.

Embodiment 44

A method of processing comprising:

contacting a medium comprising a first organic with a yeast, wherein the yeast consumes the first organic and produces a second organic.

Embodiment 45

The method of embodiment 44, wherein the first organic is selected from the group consisting of glycerol, cellobiose, xylose, lactic acid, trehalose, and an oligosaccharide.

Embodiment 46

The method of any one of embodiments 44-45, wherein the contacting reduces an amount of the first organic to less than 25% of an initial amount in the medium.

Embodiment 47

The method of any one of embodiments 44-46, wherein the second organic is selected from the group consisting of a lipid and a protein.

Embodiment 48

The method of any one of embodiments 44-47, wherein the second organic is an enzyme.

Embodiment 49

The method of any one of embodiments 44-48, further comprising, after the contacting, separating at least a portion of a component selected from the group consisting of lipid produced by the yeast, enzymes produced by the yeast, and the yeast from at least a portion of one other component of spent medium resulting from the contacting.

Embodiment 50

The method of any one of embodiments 44-49, further comprising, after the contacting, conducting a process selected from the group consisting of liquefaction of starch and saccharification of liquified starch with enzymes produced by the yeast.

Embodiment 51

The method of any one of embodiments 44-50, further comprising, after the contacting, mixing spent medium resulting from the contacting with starch and conducting liquefaction of the starch in the presence of the spent medium.

Embodiment 52

The method of any one of embodiments 44-51, wherein the medium comprises a component selected from the group consisting of glucose, glucan, trehalose, xylose, xylan, arabinose, arabinan, lactic acid, glycerol, acetic acid, butanediol, and ethanol.

Embodiment 53

The method of any one of embodiments 44-52, wherein the medium comprises a component selected from the group consisting of glucose in an amount of from about 0.1 g/L to about 10 g/L, glucan in an amount of from about 1 g/L to about 100 g/L, xylose in an amount of from about 0.1 g/L to about 10 g/L, trehalose in an amount of from about 0.01 g/L to about 100 g/L, xylan in an amount of from 0.5 g/L to about 50 g/L, arabinose in an amount of from about 0.05 g/L to about 5 g/L, arabinan in an amount of from about 0.05 g/L to about 5 g/L, lactic acid in an amount of from about 1.5 g/L to about 150 g/L, glycerol in an amount of from about 1.5 g/L to about 150 g/L, acetic acid in an amount of from about 0.05 g/L to about 5 g/L, butanediol in an amount of from about 0.2 g/L to about 20 g/L, and ethanol in an amount of from about 0.05 g/L to about 5 g/L.

Embodiment 54

The method of any one of embodiments 44-53, wherein the medium comprises a grain ethanol distillation stillage or a processed grain ethanol distillation stillage.

Embodiment 55

The method of any one of embodiments 44-45, wherein the medium comprises a processed grain ethanol distillation stillage made by processing grain ethanol distillation stillage with a step selected from the group consisting of centrifuging, removing oil, and concentrating.

Embodiment 56

The method of any one of embodiments 44-54, wherein the yeast is a lipogenic yeast.

Embodiment 57

The method of any one of embodiments 44-55, wherein the yeast is a non-genetically modified lipogenic yeast.

Embodiment 58

The method of any one of embodiments 44-56, wherein the yeast is non-genetically modified Lipomyces starkeyi.

Embodiment 59

The method of any one of embodiments 44-57, wherein the yeast is a recombinant yeast as recited in any one of embodiments 1-43. 

We claim:
 1. A recombinant yeast comprising one or more recombinant genes, wherein the one or more recombinant genes are configured to express: a diacylglycerol acyltransferase; a malic enzyme; and a glycerol-3-phosphate acyltransferase, wherein the glycerol-3-phosphate acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:40.
 2. The recombinant yeast of claim 1, wherein the yeast is a recombinant lipogenic yeast.
 3. The recombinant yeast of claim 1, wherein the yeast is a recombinant Lipomyces starkeyi.
 4. The recombinant yeast of claim 1, wherein the diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:14.
 5. The recombinant yeast of claim 4, wherein the one or more recombinant genes are further configured to express a second diacylglycerol acyltransferase, wherein the second diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:58.
 6. The recombinant yeast of claim 1, wherein the malic enzyme comprises a sequence at least about 90% identical to SEQ ID NO:34.
 7. The recombinant yeast of claim 1, wherein: the diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:14; the one or more recombinant genes are further configured to express a second diacylglycerol acyltransferase, wherein the second diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:58; and the malic enzyme comprises a sequence at least about 90% identical to SEQ ID NO:34.
 8. The recombinant yeast of claim 7, wherein the yeast is a recombinant lipogenic yeast.
 9. The recombinant yeast of claim 7, wherein the yeast is a recombinant Lipomyces starkeyi.
 10. The recombinant yeast of claim 1, wherein the recombinant genes are further configured to express a glycerol-3-phosphate dehydrogenase.
 11. A recombinant yeast comprising one or more recombinant genes, wherein the one or more recombinant genes are configured to express: a diacylglycerol acyltransferase; a malic enzyme; a glycerol-3-phosphate acyltransferase; and a glycerol-3-phosphate dehydrogenase, wherein the glycerol-3 -phosphate dehydrogenase comprises a sequence at least about 90% identical to SEQ ID NO:32.
 12. The recombinant yeast of claim 11, wherein the one or more recombinant genes are further configured to express a second glycerol-3-phosphate dehydrogenase, wherein the second glycerol-3-phosphate dehydrogenase comprises a sequence at least about 90% identical to SEQ ID NO:56.
 13. The recombinant yeast of claim 11, wherein the one or more recombinant genes are further configured to express a glycerol kinase.
 14. A recombinant yeast comprising one or more recombinant genes, wherein the one or more recombinant genes are configured to express: a diacylglycerol acyltransferase; a malic enzyme; a glycerol-3-phosphate acyltransferase; a glycerol-3-phosphate dehydrogenase; and a glycerol kinase, wherein the glycerol kinase comprises a sequence at least about 90% identical to SEQ ID NO:26.
 15. The recombinant yeast of claim 14, wherein: the diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:14; the one or more recombinant genes are further configured to express a second diacylglycerol acyltransferase, wherein the second diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:58; the malic enzyme comprises a sequence at least about 90% identical to SEQ ID NO:34; the glycerol-3-phosphate acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:40; the glycerol-3-phosphate dehydrogenase comprises a sequence at least about 90% identical to SEQ ID NO:32; and the one or more recombinant genes are further configured to express a second glycerol-3- phosphate dehydrogenase, wherein the second glycerol-3-phosphate dehydrogenase comprises a sequence at least about 90% identical to SEQ ID NO:56.
 16. The recombinant yeast of claim 15, wherein the yeast is a recombinant lipogenic yeast.
 17. The recombinant yeast of claim 15, wherein the yeast is a recombinant Lipomyces starkeyi.
 18. The recombinant yeast of claim 10, wherein the one or more recombinant genes are further configured to express an acetyl-CoA carboxylase.
 19. The recombinant yeast of claim 18, wherein the acetyl-CoA carboxylase comprises a sequence at least about 90% identical to SEQ ID NO:2.
 20. A recombinant yeast comprising one or more recombinant genes, wherein the one or more recombinant genes are configured to express: a diacylglycerol acyltransferase; a malic enzyme; a glycerol-3-phosphate acyltransferase; a glycerol-3-phosphate dehydrogenase; an acetyl-CoA carboxylase, wherein the acetyl-CoA carboxylase comprises a sequence at least about 90% identical to SEQ ID NO:2 and the acetyl-CoA carboxylase comprises a residue other than serine and threonine at a position corresponding to position 1146 of SEQ ID NO:2.
 21. The recombinant yeast of claim 18, wherein: the diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:14; the one or more recombinant genes are further configured to express a second diacylglycerol acyltransferase, wherein the second diacylglycerol acyltransferase comprises a sequence at least about 90% identical to SEQ ID NO:58; the malic enzyme comprises a sequence at least about 90% identical to SEQ ID NO:34; the glycerol-3-phosphate dehydrogenase comprises a sequence at least about 90% identical to SEQ ID NO:32; and the acetyl-CoA carboxylase comprises a sequence at least about 90% identical to SEQ ID NO:2 and the acetyl-CoA carboxylase comprises a residue other than serine and threonine at a position corresponding to position 1146 of SEQ ID NO:2.
 22. The recombinant yeast of claim 21, wherein the yeast is a recombinant lipogenic yeast.
 23. The recombinant yeast of claim 21, wherein the yeast is a recombinant Lipomyces starkeyi. 